_dictionary.title cifdic.m94 _dictionary.version 0.7.1 loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.1.1 1993-02-11 ; Highlighted all notes with # %%%%% surrounds. ; 0.1.2 1993-02-11 ; Started moving examples to *_appendix data items. ; 0.1.3 1993-02-11 ; Started moving core data names to the *_appendix data items ; 0.1.4 1993-02-11 ; Added example for _symmetry_ ; 0.1.5 1993-03-24 ; Finished moving examples to *_appendix data items ; 0.1.6 1993-03-24 ; Dealt with many issues raised by SR Hall. Some were merely typographical. Changed temp to B_iso Changed occ to occupancy Changed special_details to details. Changed asl to label everywhere. Shuffled data names in _struct_conf_ and _struct_conn_ ; 0.1.7 1993-03-24 ; Tested for Cyclops compliance - most problems are names that are too long. Changed crystal_prepration to crystal_prep Changed d_resolution to d_res Many other such changes ; 0.1.8 1993-03-25 ; Still testing for Cyclops compliance - reveal many additional syntax problems Also verified with new tool by RG Ball - still more errors fixed Dealt with issue raised by PE Bourne - amongst changes Rewrote _database_ section completely Changed _audit_contact_author_ to _audit_contact_author_name _audit_contact_author_address ; 0.1.9 1993-03-26 ; Removed _struct_topol_ section until it gets straightened out ; 0.1.10 1993-03-28 ; Filled in examples for several data categories ; 0.1.11 1993-04-03 ; Syntax checked using tools of Peter Murray-Rust - many problems fixed ; 0.1.12 1993-04-06 ; More syntax problems fixed a la Peter Murray-Rust ; 0.1.13 1993-04-07 ; Introduced _exptl_crystal_grow_ data names ; 0.1.14 1993-04-07 ; Experiment with refers_to, category and part_of_key in entity_conn_atom_ and entity_conn_bond_ sections. Discovered horror show with nonconcurrent versions on different computers - not yet resolved. ; 0.1.15 1993-05-09 ; Reconciled nonconcurrent versions Removed trailing blanks Made corrections based on email suggestions from P. Bourne ; 0.1.16 1993-05-10 ; Made corrections based on written comments from K. Watenpaugh Made corrections/additions based on discussions at Rutgers ; 0.1.17 1993-05-11 ; Changed _atom_site_label_component_? to new nomenclature Introduced category DDL throughout Introduced refers_to DDL throughout Introduced part_of_key DDL throughout Mandated that _list must be in each data definition Standardized 'need not be unique' statements Standardized example headers ; 1.1.18 1993-05-12 ; Looped out authors and editors in citation list Verified with RGB tools Some style consistency imposed Fleshed out category definitions and imposed style Updated "sets of data item" at beginning of document Checked alphabetical order of data names - moved id's ; 0.2.1 1993-05-13 ; Major rethinking of _entity_ data based following discussions of 1993-05-10 meeting ; 0.2.2 1993-05-18 ; Style consistency and proof reading changes throughout Make page numbers general to articles and chapters in citation Added *_method to all phasing categories Looped out keywords from _struct_site_ list Added _atom_site_label_ definitions as per H. Berman Added _struct_biol_view_ and struct_site_view_ items as per P. Bourne Added _atom_sites_alt_ data items to formally handle alternative conformations Verified with Cyclops and RGB tools ; 0.2.3 1993-05-19 ; Fixed based on problems unearthed by Peter Murray-Rust and Brian McMahon ; 0.2.4 1993-05-20 ; DDL adjustment from down under ):-(> ; 0.2.5 1993-05-20 ; A general merging of updates from PMR, BMcM and SRH Fixed typographical and stylistic problems a la BMcM ; 0.2.6 1993-06-02 ; Fixed _atom_site_ example (_entity_poly_seq_num) Removed _list_link_parent from _entity_mon_atom_atom_id a _entity_nonp_atom_atom_id Added real APS coordinates to _atom_site_ example Rewrote _atom_sites_footnote_ example ; 0.2.7 1993-08-01 ; Redesigned phasing_MIR definitions ; 0.2.8 1993-08-03 ; More work on phasing_MIR Created phasing_MIR_der and phasing_MIR_der_shell categories ; 0.3.1 1993-08-08 ; Began implementing DDL v0.7 ; 0.3.2 1993-08-11 ; Cleaning up of stray notes ; 0.3.3 1993-08-12 ; Syntax and consistency checks - SRH Added _type of null for appendix items. ; 0.3.4 1993-09-01 ; Added _struct_conn_ptnr1_label_alt_id and _struct_conn_ptnr2_label_alt_id Corrected definitions for _struct_conn_ptnr2_ items Added _struct_site_gen_label_alt_id Fixed Cullis reference in _phasing_MIR_der_shell_R_Cullis Change _database_PDB_rev_ example to _loop construction Added _PDB_remark category (data items _PDB_remark_num and _PDB_remark_text) Added 'obsolete' to enumeration list for _database_PDB_rev_status Added _database_PDB_rev_replaces data item ; 0.3.5 1993-09-08 ; Added missing _diffrn_orient_matrix_UB_33 (in appendix) Added missing _phasing_MIR_der_shell_der_id to appropriate example ; 0.3.6 1993-10-10 ; Changed *_appendix to *_[mm] throughout Removed 'Need example here' from _chemical_[mm] Removed 'Need example here' from _chemical_conn_atom_[mm] Removed 'Need example here' from _chemical_conn_bond_[mm] Moved _PDB to end of all relevant data names (except _[mm]) Added _database_rev_record_details_PDB data name Changed _refine_occupancy_limit_high to _refine_occupancy_max Changed _refine_occupancy_limit_low to _refine_occupancy_min Changed _refine_B_iso_limit_high to _refine_B_iso_max Changed _refine_B_iso_limit_low to _refine_B_iso_min Changed all definitions and examles in _refine_iso_B_ category to _refine_B_iso_ equivalents ; 0.3.7 1993-11-16 ; Changed form of dates in _update_history to CIF style Changed ? to . in examples, where appropriate Added _example_detail to _refine_ls_restr_type Expanded definition of _refine_ls_restr_type ; 0.3.8 1993-11-30 ; Moved _audit_author_, _citation_ categories to CIF core Definitions and small-molecule examples removed from *_[mm] sections that don't extend core categories - BMcM ; 0.3.9 1993-12-02 ; Deleted section summarizing categories - PMDF Returned definitions for most *_[mm] sections - PMDF Added _list and _list_level to global - PMDF Changed form of dates from yy-mm-dd to yyyy-mm-dd - PMDF Checked lists of data items in core, fixing some problems with missing names and alphabetization - PMDF Resorted some categories to correct alphabetization - PMDF Changed form and definitions of _database_remark_num_PDB and _database_remark_text_PDB - PMDF Added data item _database_rev_replaced_by_PDB - PMDF Reordered data items in _citation example - PMDF Added data item _exptl_crystal_density_%_sol - PMDF ; 0.3.10 1993-12-15 ; Various changes following suggestions from BMcM Refined definition of _atoms_site_label_atom_id - PMDF Removed _atom_sites_fract_tran (moved to core) - PMDF Changed _diffrn_crystal_physical_device to _diffrn_crystal_support - PMDF Changed _diffrn_measure_device_part to _diffrn_measure_device_specific - PMDF Changed _diffrn_rad_detector_part to _diffrn_rad_detector_specific - PMDF Changed _diffrn_rad_source_part to _diffrn_rad_source_specific - PMDF Changed *_par1* and *_par2* to *_ptnr* in _struct_conn* - PMDF Fixed several occurrences of \&A instead of \%A - PMDF ; 0.3.11 1993-12-22 ; Made a number of fixes relayed by PEB from MS AND RH _type of _atom_site_footnote_id (numb->char) - PMDF _type of _database_rev_record_rev_num_PDB (char->numb) - PMDF _type of _phasing_MIR_der_number_of_sites (char->numb) - PMDF save_atom_sites_fract_tran_matrx to _matrix - PMDF _type of _phasing_MIR_site_details (numb->char) - PMDF _example of _struct_conf_type_reference - PMDF ; 0.3.12 1993-12-23 ; Broke out examples from intro sections to loop_ _item_examples.case _example_detail construction - BMcM ; 0.3.13 1994-01-13 ; Rationalisation of categories between mm and core dicts - BMcM Deleted _diffrn_crystal_environment (same as core _diffrn_ambient_environment) and moved other _diffrn_crystal items to core - BMcM Fixed typos, removed hyphenation ("be kind to ciftex") - BMcM Some re-alphabetization - BMcM ; 0.3.14 1994-01-26 ; Lots more re-alphabetization - PMDF Changed non_s to nstd throughout - PMDF Changed nonp to npol throughout - PMDF Removed all multiple spaces - PMDF Fixed a couple of alignment problems - PMDF ; 0.4.1 1994-02-04 ; Major modifications of _entity_ subcategories - PMDF Added angles, planes, torsion angles and chiral centers to _entity_mon_ and _entity_npol_ Added many missing definitions Added many missing examples ; 0.4.2 1994-02-25 ; Corrected spelling errors found by BMcM - PMDF ; 0.4.3 1994-03-28 ; Various changes following suggestions by IDB - PMDF Changed _entity_mon_angle_value to _entity_mon_angle_value_angle in example Changed save_entity_npol_bond_value to save_entity_npol_bond_value_dist Changed nonp to npol in _entity_npol_tor_value category Reworded angle _enumeration_details in _refine_ls_restr_type Reworded defintions in _struct_asym_[mm] and _struct_biol_[mm] Reworded definitions of _struct_conn_symmetry_* _struct_site_gen_symmetry _struct_biol_gen_symmetry Split _struct_conn_symmetry_* into _struct_conn_ptnr1_symmetry and _struct_conn_ptnr2_symmetry Split _struct_conn_role_* into _struct_conn_ptnr1_role and _struct_conn_ptnr2_role Removed _list_link_child from _struct_conn_conn_type_id Added _list_link_child to _struct_conn_type_id ; 0.5.1 1994-10-10 ; Implementation of Treaty of Brussels - PMDF Merged CIF core dated 1994-03-01 (from BMcM) with mm dictionary dated 1994-05-20. The history records for the core dictionary are included here to identify the version of the core that was merged: _dictionary_name cifdic.c94 _dictionary_version 2.0 _dictionary_update 1994-03-01 _dictionary_history 1991-05-27 Created from CIF Dictionary text. SRH 1991-05-30 Validated with CYCLOPS & CIF ms. SRH 1991-06-03 Adjustments to some definitions. SRH 1991-06-06 Adjustments a la B. McMahon. SRH 1991-06-18 Additions & some redefinitions. SRH 1991-07-04 Corrected 90:0 in *_detect_slit_. SRH 1991-09-20 Additions & some redefinitions. SRH 1991-09-20 Final published version. IUCr 1991-11-12 Add _diffrn_ambient_environment. SRH 1991-11-12 Allow 'c' for _atom_site_calc_flag. SRH 1993-02-23 Apply global_ and 'unknown' -> '?' SRH 1993-03-05 Changes resulting from MM dictionary. SRH 1993-05-20 Changes arising from new DDL commands. SRH 1993-08-05 Additional finetuning pre-Beijing. SRH 1993-12-22 Introductory sections added to categories. BMcM 1993-12-22 Additional categories from mm work: _audit_author, _citation, _atom_sites_fract_tran_matrix. BMcM 1994-03-01 Add 'undef' to _refine_ls_hydrogen_treatment. BMcM 1994-03-01 Add '_publ_section_exptl_prep' and '*_refinement'. BMcM 1994-03-01 Add 'atom_site_aniso_ratio'. BMcM -------------- Removed all mm sections that enumeration items present in core but not present in mm dictionary. Fixed errors with missing trailing _'s in some category headers Also unbalanced ##'s in same place Removed "End of Example" statement everywhere Standardized syntax for missing examples Standardized syntax and style for category _definition data items. Added a bunch of ending dashed lines where they were missing.Merged [] and [mm] category explanation sections. Made HIV example always example 1, moved examples from core (where they were different from the HIV example) to higher numbers. Changed data_ to save_ everywhere Changed _name to _item.name everywhere Added _item.mandatory_code everywhere Added save_ everywhere Moved _description to top of _save frame everywhere Changed _example to _item_examples.case everywhere Changed _example_detail to _item_examples.detail everywhere Changed _description to _item.description.description everywhere Removed _list yes everywhere Removed _list_reference everywhere Changed _enumeration_range to enumeration_limit.minimum and enumeration_limit.maximum everywhere ; 0.5.4 1994-11-14 ; Implementation of DDL 2.0.7 dictionary wide - PMDF Changed _enumeration to _enumeration.code Changed _enumeration_detail to _enumberation.code_detail Changed _enumeration_default to _enumeration_default.code Put .'s in item names (incomplete) Moved _PDB back to appropriate place in item names in the _database_remark_PDB_ and _database_rev_PDB_ and _database_rev_record_PDB_ categories Changed database_rev_PDB to database_PDB_rev Changed database_remark_PDB to database_PDB_remark Changed database_rev_record_PDB to database_PDB_rev_record Changed category items from item to category Began getting rid of *_whatever construction in category and item descriptions ; 0.5.5 1994-11-15 ; Implementation of DDL 2.0.7 dictionary wide - PMDF Finished putting .'s in itme names Changed _diffrn_measure_ to _diffrn_measurement. Changed _diffrn_rad_ to _diffrn_radiation. Implemented category and id pointers for entity category. Found all sorts of errors while doing this, and attempted to fix them consistently. Did not remove child data Items, even though they don't have to be specified - they should help keep all of this straight during the transition. Some silly reformatting to ensure that data values always have the first alphabetic character in column 33. More silly reformatting to put each example in an example loop on a separate line. ; 0.6.1 1994-11-21 ; Changes (JDW): + Converted dictionary and dictionary_history categories. Incorporated core dictionary history list into the new history list in the revision 0.5.1 where the dictionary merger is firsted discussed. ; 0.6.2 1994-11-28 ; Changes (PMDF): + Made loop_ _item.name data items into separate data items This involved rewriting the definitions of most of them. In doing so I continued to eliminate the a.b_* construction. Added unit type of degrees. Added unit type of minutes. Added unit type of electrons. ; 0.6.2 1994-11-30 ; Changes (PMDF): + Finished conversion of units data items Added a number of unit types to the table Conversation table still need to be fleshed out Removed _list_mandatory and changed _item_mandatory.code to yes for those data items ; 0.6.3 1994-12-01 ; Changes (PMDF): + Began conversion of _list_link_parent items to appropriate new DDL relationships ; 0.6.4 1994-12-02 ; Changes (PMDF): + Began implementation of new scheme for relationships in the entity category All entities will be treates as polymers - non-polymers will have a number of monomers of 1 All data items in ENTITY_NPOL categories are elminated All data items in ENTITY_POLY category are moved to ENTITY ; 0.6.5 1994-12-06 ; Changes (PMDF): + Finished conversion of _list_link_parent items to appropriate new DDL relationships Filled out category_key.id items in each category Had to add diffrn_refln.id item, as cannot use h k l in that category (perfectly valid to measure same relfection more than once). Used _diffrn_standard_refln.code in that category - this may cause a problem with old files, as example file did not give this data item Moved _entity_poly items back to _entity category Moved _entity_poly.formula_weight to entity.formula_weight Used _exptl_crystal.id in that category - this may cause a problem with old files, as example file did not give this data item Added _exptl_crystal_grow.crystal_id in that category Added _symmetry_equiv.id in that category - this may cause a problem with old files, as this is a new data item ; 0.6.6 1994-12-07 ; Changes (PMDF): + Created DATABASE_NEW category to solve logical problems with old DATABASE category. Need to think some more about how old data items are handled. Added aliases for remaining c91 data items Changed geom_angle to geom_angle.value (aliased to original name) Changed geom_torsion to geom_torsion.value (aliased to original name) Returned ATOM_SITE items taken out during ATOM_SITE_MM transition ; 0.6.7 1994-12-08 ; Changes (PMDF): + Created ATOM_SITE_ANISOTROP category to provide for ability to have aniostropic data is a separate loop, if desired. Checked and fixed a bunch of style things Added item_units.code of degrees in data items with degrees in the description but not in the ddl Added item_units.code of kelvin in data items with kelvin in the description but not in the ddl (and added 'in degrees kelvin' to the description of those with item_units.code of kelvin but no corresponding phrase in the description) Added item_units.code of microseconds to _diffrn_radiation.detector_dtime (added to units list at same time) Added 'in minutes' to description of _diffrn_refln.elapsed_time Added 'in kilopascals' to to the description of those with item_units.code of kilopascals but no corresponding phrase in the description Added BLOCK category Added appopriate pointers (in category key, and with a data item pointing to _block.id) in all categories that needed them ; 0.6.8 1994-12-09 ; Changes (PMDF): + Added _esd data items where needed Rationalized descriptions for all of the coordinate data items ; 0.6.9 1994-12-13 ; Changes (PMDF): + Established check-list for unfinished tasks and began dealing with them Added enumeration limits of 0 and 1 and enumeration default of 1.0 to occupancy data items Left heavy-atom maximum with an enumeration of ? Added enumeration default of 1_555 to all _symmetry data items where it was missing Changed 'connect type' to 'interaction' in _struct_conn_type data items. Filled out sub_category ddl items for cartesian coordinates, fractional coordinates, cartesian coordinates esds, and Miller indices. ; 0.6.10 1994-12-14 ; Changes (PMDF): + Fixed R-Kraut reference Changed _reflns_shell.possible_&_all to _reflns_shell.percent_possible_all Changed _reflns_shell.possible_&_obs to _reflns_shell.percent_possible_obs Changed _exptl_crystal.density_%_sol to _exptl_crystal.density_percent_sol Included full formula for this calculation in description Changed _refine_ls_restr.model _refine_ls_restr.dev_ideal Changed _refine_ls_restr.target _refine_ls_restr.dev_ideal_target Improved wording of all definitions in REFINE_LS_RESTR Explained sums in _reflns_shell.Rmerge_I_obs and related data items ; 0.6.11 1994-12-15 ; Changes (PMDF): + Changed _enumeration_default.code to _item_default.value Changed _enumeration_default.value to _item_default.value Changed _enumeration.code to _item_enumeration.value Changed _enumeration.detail to _item_enumeration.detail Changed _enumeration.case to _item_enumeration.value Changed _enumeration_limit.maximum to _item_range.maximum Changed _enumeration_limit.minimum to _item_range.minimum Checked that matrix were properly labelled as either rw_rowwise or just plan rowwise. Reworded matrix descriptions for consistency. Got rid of the last of the a.b_* constructions in descriptions Added cell_length, cell_length_esd, cell_angle and cell_angle_esd subcategories Changed special_details to details for core items - original names retained in aliases Added atom_site.id Added mm_atom_site_label subcategory Commented out _atom_site.label_component until it can be dealt with properly Changed 'SIF' to 'data block' in a number of descriptions. ; 0.6.12 1994-12-16 ; Changes (PMDF): + Added data item _refln.R_free_status Added data item _reflns.R_free_details Changed _refine_ls_shell.reflns to refine_ls_shell.number_obs Added _refine_ls_shell.number_R_free Added _refine_ls_shell.number_all Added _refine_ls_shell.R_factor_R_free Added _refine_ls_shell.wR_factor_R_free Tidied up the count and R-factor descriptions in REFINE_LS_SHELL Added appropriate item_related names to the R-factors in REFINE_LS_SHELL Changed 'count' to 'number' in several data names Changed _reflns.number_total to _reflns.number_all Changed _reflns.number_observed to _reflns.number.obs Added _refine.ls_R_factor_R_free Added _refine.ls_wR_factor_R_free Edited descriptions of the other R-factor data items in the REFINE category to conform to the style in REFINE_LS_SHELL Re-alphabetized the things I changed yesterday from special_details to details - I had forgotten to do that yesterday ; 0.6.13 1994-12-19 ; Changes (PMDF): + Changed refine.ls_number_reflns to refine.ls_number_reflns_obs Added refine.ls_number_reflns_all Added refine.ls_number_reflns_R_free Changed _refln.observed_status to refln.status Expanded enumeration list to include resolution limits and R-free flag Rewrote definition Eliminated refln.R_free_status Changed _refine_ls_shell.number_all to _refine_ls_shell.number_reflns_all Changed _refine_ls_shell.number_obs to _refine_ls_shell.number_reflns_obs Changed _refine_ls_shell.number_R_free to _refine_ls_shell.number_reflns_R_free Added PHASING category Filled in and reformatted units conversion table ; 0.7.1 1994-12-19 ; Changes (JDW): + First pass through SIFLIB checking tools. Corrected syntax errors and missing parent references. ; 0.7.2 1994-12-20 ; Changes (PMDF): + Merged JDW changes with version 0.6.12 Changed _item_type.code of numb to either int or float Changed _item_description.descrption to category.description where appropriate Fixed a bunch of pure syntax errors Removed 'refln_scale_group' from list of category groups. Changed _refln_scale_group_code to _refln.scale_group_code somewhere Changed REFLN_SCALE_GROUP_CODE to _refln.scale_group_code somewhere Reformatted CATEGORY_GROUP_LIST items to match style of other header categories Ensures that all _category data items obey they rule of first alphabetic character is column 34 (most didn't before this check) Removed _item_related stuff from _atom_site.aniso_U[1][1] (at the rest) data items, and added wording to description that these items are only there for compliance via the alias (but left in the one _item_related thing that made the matrix element data item alternate exclusive to the full matrix data item Added language about compliance to _atom_sites.cartn.tran.matrix Added language about compliance to _diffrn_orient_matrix.UB Added language about compliance to _diffrn_reflns.transf_matrix Removed matrix element data items for _atom_sites.fract.tran.matrix - this wasn't in c91 and so doesn't need aliasing ; 0.7.3 1994-12-22 ; Changes (PMDF): + Fixed things turned up by JDW checking of 0.7.2 Couple of small typos Added angstroms_cubed to units list and conversion tables Added _phasing_MIR_site.atom_type_symbol and added this reference to the table until _atom_type.symbol Added _entity_mon_atom.substruct_code Began adding STRUCT_MON_PROT, but this is not yet complete ; 0.7.4 1995-01-12 ; Changes (PMDF): + Finished working on STRUCT_MON_PROT category Added STRUCT_MON_DETAILS category Added STRUCT_MON_PROT_CIS category Added STRUCT_NCS_ENS category Added STRUCT_NCS_ENS_OPER category Added STRUCT_NCS_DOM category Added STRUCT_NCS_DOM_GEN category Added equations to definitions of _phasing_MIR_der_shell.fom and _phasing_MIR_shell.fom Added REFINE_HIST category ; 0.7.5 1995-01-13 ; Changes (PMDF): + Provided for sequence microheterogenity by making _entity_poly_seq.mon_id part of the category key and by adding the data item _entity_poly_seq.hetero as a flag Added ENTITY_POLY_SEQ_DIF category - this meant adjusting some pointer in referenced data items. Added _entity_mon_atom.alt_atom_id. Added COMP_PROG category Removed non-c91 COMPUTING data items (phasing averaging, MAD, MIR and MR) ; 0.7.6 1995-01-17 ; Changes (PMDF): + Added ENTITY_SRC_NAT category Added ENTITY_SRC_GEN category Added ENTITY_NAM_COM category Added ENTITY_NAM_SYS category Added _entity.src_method data item Moved other entity data items to new categories as appropriate ; 0.7.7 1995-01-18 ; Changes (PMDF): + Added PHASING_MIR_REFLN category ; 0.7.8 1995-01-25 ; Changes (PMDF): + Added _entity_mon.type, _entity_mon.number_atoms_all, _entity_mon.number_atoms_nh, _entity_mon.one_letter_code Added _entity_mon_angle.value_angle_esd, _entity_mon_angle.value_dist_esd, _entity_mon_bond.value_dist_esd Added _entity_mon_atom.type_energy, but since this is intended to be a pointer to a category (_atom_type_energy) that doesn't exist yet, have left it commented out Added _entity_mon_chir.volume_three, _entity_mon_chir.volume_three_esd and _entity_mon_chir.volume_flag Added _entity_mon_plane.number_atoms_all, _entity_mon_plane.number_atoms_nh Added _entity_mon_chir.number_atoms_all, _entity_mon_chir.number_atoms_nh Added _entity_mon_chir_atom.dev Added _entity_mon_tor_value.angle_esd, _entity_mon_tor_value.dist_esd Added ENTITY_LINK category Added ENTITY_LINK_ANGLE category Added ENTITY_LINK_BOND category Changes (HB et al.): + Added STRUCT_MON_NUCL category Changes (PMDF): + Added label links from STRUCT_MON_NUCL to rest of dictionary Added label links from STRUCT_MON_PROT as well (forget them initially) ; loop_ _sub_category.id _sub_category.description 'cartesian_coordinate' ; The collection of x, y, and z components of a position specified with references to a Cartesian (orthonal Angstrom) coordinate system. ; 'cartesian_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with references to a Cartesian (orthogonal Angstrom) coordinate system. ; 'fractional_coordinate' ; The collection of x, y, and z components of a position specified with references to unit cell directions. ; 'fractional_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with references to unit cell directions. ; 'miller_index' ; The collection of h, k, and l components of a the Miller index of a reflection. ; 'cell_length' ; The collection of a, b, and c axis lengths of a unit cell. ; 'cell_length_esd' ; The collection of estimated standard deviations of the a, b, and c axis lengths of a unit cell. ; 'cell_angle' ; The collection of alpha, beta, and gamma angles of a unit cell. ; 'cell_angle_esd' ; The collection of estimated standard deviations of the alpha, beta, and gamma angles of a unit cell. ; 'mm_atom_site_label' ; The collection of alt id, asym id, atom id, res id and seq id components of the label for a macrmomolecular atom site. ; loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.description code char '[A-Za-z0-9,.;:"&<>/\{}`~!@#$%]*' ; code item types ... ; char char '[A-Za-z0-9,.;:"&<>?/\{}`~!@#$% ]*' ; char item types ... ; text char '[A-Za-z0-9,.;:"&<>?/\{}`~!@#$% \n]*' ; text item types ... ; int numb '[0-9]+' ; int item types are the subset of numbers that are the negative or positive integeters. ; float numb '-?(([0-9]+)|([0-9]*\.[0-9]+)([eE][-+]?[0-9]+)?)' ; int item types are the subset of numbers that are the floating numbers. ; name uchar '_[A-Za-z0-9_]+\.[A-Za-z0-9_]+' ; name item types take the form... ; idname uchar '[A-Za-z0-9_]+' ; idname item types take the form... ; any char '[A-Za-z0-9,.;:"&<>?/\{}`~!@#$% \n]*' ; idname item types take the form... ; date char ; {_dictionary_history.update_year}- {_dictionary_history.update_month}- {_dictionary_history.update_day} ; ; date item types take the form... ; symop char '[1-192]\_[1-9][1-9][1-9]' ; symop item types takes the form n_mmm, where 'n' is the value of _symmetry_equiv.id that corresponds to the relevant value of _symmetry_equiv.pos_as_xyz and 'mmm' are the concatenated cell translations along x, y, z with respect to the base number 555. The symmetry transformation is applied to the fractional coordinates in the ATOM_SITE category identified by _atom_site_label. If there are no cell translations the translation number may be omitted. ; loop_ _item_structure_list.code _item_structure_list.index _item_structure_list.dimension 'matrix3x3' 0 3 'matrix3x3' 1 3 loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' . ; Categories that belong to the macromolecular dictionary. ; 'atom_group' 'inclusive_group' ; Categories that describe the properties of atoms. ; 'audit_group' 'inclusive_group' ; Categories that describe dictionary maintenance and identification. ; 'block_group' 'inclusive_group' ; Categories that pertain to the entire data block ; 'cell_group' 'inclusive_group' ; Categories that describe the unit cell. ; 'chemical_group' 'inclusive_group' ; Categories that describe chemical properties and nomenclature. ; 'citation_group' 'inclusive_group' ; Categories that provide bibliographic references ; 'computing_group' 'inclusive_group' ; Categories that describe the computational details of the experiment. ; 'compliance_group' 'inclusive_group' ; Categories that are included in this dictionary specifically to comply with previous dictionaries. ; 'database_group' 'inclusive_group' ; Categories that hold references to other databases with related information. ; 'diffrn_group' 'inclusive_group' ; Categories that describe details of the diffraction experiment. ; 'entity_group' 'inclusive_group' ; Categories that describe chemical entities ; 'exptl_group' 'inclusive_group' ; Categories which hold details of the experimental conditions. ; 'geom_group' 'inclusive_group' ; Categories which hold internal coordinates. ; 'journal_group' 'inclusive_group' ; Categories which are used for internal processing by the publication staff. ; 'phasing_group' 'inclusive_group' ; Categories that describe phasing. ; 'publ_group' 'inclusive_group' ; Categories that describe manuscript submission. ; 'refine_group' 'inclusive_group' ; Categories that describe refinement. ; 'refln_group' 'inclusive_group' ; Categories that describe the details of reflection measurements. ; 'struct_group' 'inclusive_group' ; Categories that contain details about the crystallographic structure. ; 'symmetry_group' 'inclusive_group' ; Categories that describe symmetry information. ; loop_ _item_units_list.code _item_units_list.detail 'centimetres' 'centimetres (meters * 10^( -2))' 'millimetres' 'millimetres (meters * 10^( -3))' 'nanometres' nanometres (meters * 10^( -9)) 'angstroms' 'angstroms (meters * 10^(-10))' 'picometres' 'picometres (meters * 10^(-12))' 'reciprocal_centimetres' 'reciprocal centimetres (meters * 10^( -2)^-1)' 'reciprocal_millimetres' 'reciprocal millimetres (meters * 10^( -3)^-1)' 'reciprocal_nanometres' 'reciprocal nanometres (meters * 10^( -9)^-1)' 'reciprocal_angstroms' 'reciprocal angstroms (meters * 10^(-10)^-1)' 'reciprocal_picometres' 'reciprocal picometres (meters * 10^(-12)^-1)' 'nanometres_squared' 'nanometres squared (meters * 10^( -9))^2' 'angstroms_squared' 'angstroms squared (meters * 10^(-10))^2' 'picometres_squared' 'picometres squared (meters * 10^(-12))^2' 'nanometres_cubed' 'nanometres cubed (meters * 10^( -9))^3' 'angstroms_cubed' 'angstroms cubed (meters * 10^(-10))^3' 'picometres_cubed' 'picometres cubed (meters * 10^(-12))^3' 'kilopascals' 'kilopascals' 'gigapascals' 'gigapascals' 'hours' 'hours' 'minutes' 'minutes' 'seconds' 'seconds' 'microseconds' 'microseconds' 'degrees' 'degrees (of arc)' 'celsius' 'degrees (of temperature) Celsius' 'kelvin' 'degrees (of temperature) Kelvin' 'electrons' 'electrons' 'electrons_squared' 'electrons squared' 'electrons_per_nanometres_cubed' ; electrons per nanometres cubed (meters * 10^( -9))^3 ; 'electrons_per_angstroms_cubed' ; electrons per angstroms cubed (meters * 10^(-10))^3 ; 'electrons_per_picometres_cubed' ; electrons per picometres cubed (meters * 10^(-12))^3 ; loop_ _units_conversion.from_code _units_conversion.to_code _units_conversion.operator _units_conversion.factor 'centimetres' 'millimetres' '*' 1.0E+01 'centimetres' 'nanometres' '*' 1.0E+07 'centimetres' 'angstroms' '*' 1.0E+08 'centimetres' 'picometres' '*' 1.0E+10 'millimetres' 'centimetres' '*' 1.0E-01 'millimetres' 'nanometres' '*' 1.0E+06 'millimetres' 'angstroms' '*' 1.0E+07 'millimetres' 'picometres' '*' 1.0E+09 'nanometres' 'centimetres' '*' 1.0E-07 'nanometres' 'millimetres' '*' 1.0E-06 'nanometres' 'angstroms' '*' 1.0E+01 'nanometres' 'picometres' '*' 1.0E+03 'angstroms' 'centimetres' '*' 1.0E-08 'angstroms' 'millimetres' '*' 1.0E-07 'angstroms' 'nanometres' '*' 1.0E-01 'angstroms' 'picometres' '*' 1.0E+02 'picometres' 'centimetres' '*' 1.0E-10 'picometres' 'millimetres' '*' 1.0E-09 'picometres' 'nanometres' '*' 1.0E-03 'picometres' 'angstroms' '*' 1.0E-02 'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01 'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07 'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08 'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10 'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01 'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06 'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07 'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09 'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07 'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06 'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01 'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03 'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08 'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07 'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01 'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02 'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10 'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09 'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03 'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01 'nanometres_squared' 'angstroms_squared' '*' 1.0E+02 'nanometres_squared' 'picometres_squared' '*' 1.0E+06 'angstroms_squared' 'nanometres_squared' '*' 1.0E-02 'angstroms_squared' 'picometres_squared' '*' 1.0E+04 'picometres_squared' 'nanometres_squared' '*' 1.0E-06 'picometres_squared' 'angstroms_squared' '*' 1.0E-04 'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03 'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09 'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03 'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06 'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09 'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06 'kilopascals' 'gigapascals' '*' 1.0E-06 'gigapascals' 'kilopascals' '*' 1.0E+06 'hours' 'minutes' '*' 6.0E+01 'hours' 'seconds' '*' 3.6E+03 'hours' 'microseconds' '*' 3.6E+09 'minutes' 'hours' '/' 6.0E+01 'minutes' 'seconds' '*' 6.0E+01 'minutes' 'microseconds' '*' 6.0E+07 'seconds' 'hours' '/' 3.6E+03 'seconds' 'minutes' '/' 6.0E+01 'seconds' 'microseconds' '*' 1.0E+06 'microseconds' 'hours' '/' 3.6E+09 'microseconds' 'minutes' '/' 6.0E+07 'microseconds' 'seconds' '/' 1.0E+06 'celsius' 'kelvin ' '-' 273.0 'kelvin' 'celsius' '+' 273.0 'electrons_per_nanometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E-03 'electrons_per_nanometres_cubed' 'electrons_per_picometres_cubed' '*' 1.0E-09 'electrons_per_angstroms_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E+03 'electrons_per_angstroms_cubed' 'electrons_per_picometres_cubed' '*' 1.0E-06 'electrons_per_picometres_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E+09 'electrons_per_picometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E+06 save_ATOM_SITE save_atom_site.aniso_B save_atom_site.aniso_B_esd save_atom_site.aniso_ratio save_atom_site.aniso_U save_atom_site.aniso_U_esd save_atom_site.aniso_U[1][1] save_atom_site.aniso_U[1][2] save_atom_site.aniso_U[2][2] save_atom_site.aniso_U[1][3] save_atom_site.aniso_U[2][3] save_atom_site.aniso_U[3][3] save_atom_site.attached_hydrogens save_atom_site.B_iso_or_equiv save_atom_site.B_iso_or_equiv_esd save_atom_site.calc_attached_atom save_atom_site.calc_flag save_atom_site.cartn_x save_atom_site.cartn_x_esd save_atom_site.cartn_y save_atom_site.cartn_y_esd save_atom_site.cartn_z save_atom_site.cartn_z_esd save_atom_site.chemical_conn_number save_atom_site.constraints save_atom_site.description save_atom_site.disorder_group save_atom_site.entity_id save_atom_site.entity_seq_num save_atom_site.footnote_id save_atom_site.fract_x save_atom_site.fract_x_esd save_atom_site.fract_y save_atom_site.fract_y_esd save_atom_site.fract_z save_atom_site.fract_z_esd save_atom_site.group_PDB save_atom_site.id save_atom_site.label save_atom_site.label_alt_id save_atom_site.label_asym_id save_atom_site.label_atom_id save_atom_site.label_res_id save_atom_site.label_seq_id save_atom_site.occupancy save_atom_site.occupancy_esd save_atom_site.refinement_flags save_atom_site.restraints save_atom_site.symmetry_multiplicity save_atom_site.thermal_displace_type save_atom_site.type_symbol save_atom_site.U_iso_or_equiv save_atom_site.U_iso_or_equiv_esd save_atom_site.Wyckoff_symbol save_ATOM_SITE_ANISOTROP save_atom_site_anisotrop.B save_atom_site_anisotrop.B_esd save_atom_site_anisotrop.label save_atom_site_anisotrop.ratio save_atom_site_anisotrop.type_symbol save_atom_site_anisotrop.U save_atom_site_anisotrop.U_esd save_ATOM_SITES save_atom_sites.block_id save_atom_sites.cartn_tran_matrix save_atom_sites.cartn_tran_matrix[1][1] save_atom_sites.cartn_tran_matrix[1][2] save_atom_sites.cartn_tran_matrix[1][3] save_atom_sites.cartn_tran_matrix[2][1] save_atom_sites.cartn_tran_matrix[2][2] save_atom_sites.cartn_tran_matrix[2][3] save_atom_sites.cartn_tran_matrix[3][1] save_atom_sites.cartn_tran_matrix[3][2] save_atom_sites.cartn_tran_matrix[3][3] save_atom_sites.cartn_transform_axes save_atom_sites.frac_tran_matrix save_atom_sites.solution_primary save_atom_sites.solution_secondary save_atom_sites.solution_hydrogens save_ATOM_SITES_ALT save_atom_sites_alt.details save_atom_sites_alt.id save_ATOM_SITES_ALT_ENS save_atom_sites_alt_ens.details save_atom_sites_alt_ens.id save_ATOM_SITES_ALT_GEN save_atom_sites_alt_gen.alt_id save_atom_sites_alt_gen.ens_id save_ATOM_SITES_FOOTNOTE save_atom_sites_footnote.id save_atom_sites_footnote.text save_ATOM_TYPE save_atom_type.analytical_mass_ save_atom_type.description save_atom_type.number_in_cell save_atom_type.oxidation_number save_atom_type.radius_bond save_atom_type.radius_contact save_atom_type.scat_Cromer_Mann_a1 save_atom_type.scat_Cromer_Mann_a2 save_atom_type.scat_Cromer_Mann_a3 save_atom_type.scat_Cromer_Mann_a4 save_atom_type.scat_Cromer_Mann_b1 save_atom_type.scat_Cromer_Mann_b2 save_atom_type.scat_Cromer_Mann_b3 save_atom_type.scat_Cromer_Mann_b4 save_atom_type.scat_Cromer_Mann_c save_atom_type.scat_dispersion_imag save_atom_type.scat_dispersion_real save_atom_type.scat_source save_atom_type.scat_versus_stol_list save_atom_type.symbol save_AUDIT save_audit.creation_date save_audit.creation_method save_audit.revision_id save_audit.update_record save_AUDIT_AUTHOR save_audit_author.address save_audit_author.name save_AUDIT_CONTACT_AUTHOR save_audit_contact_author.address save_audit_contact_author.email save_audit_contact_author.fax save_audit_contact_author.name save_audit_contact_author.phone save_BLOCK save_block.id save_CELL save_cell.angle_alpha save_cell.angle_alpha_esd save_cell.angle_beta save_cell.angle_beta_esd save_cell.angle_gamma save_cell.angle_gamma_esd save_cell.block_id save_cell.details save_cell.formula_units_Z save_cell.length_a save_cell.length_a_esd save_cell.length_b save_cell.length_b_esd save_cell.length_c save_cell.length_c_esd save_cell.volume save_cell.volume_esd save_CELL_MEASUREMENT save_cell_measurement.block_id save_cell_measurement.pressure save_cell_measurement.pressure_esd save_cell_measurement.radiation save_cell_measurement.reflns_used save_cell_measurement.temperature save_cell_measurement.temperature_esd save_cell_measurement.theta_max save_cell_measurement.theta_min save_cell_measurement.wavelength save_CELL_MEASUREMENT_REFLN save_cell_measurement_refln.index_h save_cell_measurement_refln.index_k save_cell_measurement_refln.index_l save_cell_measurement_refln.theta save_CHEMICAL save_chemical.block_id save_chemical.compound_source save_chemical.melting_point save_chemical.name_common save_chemical.name_mineral save_chemical.name_structure_type save_chemical.name_systematic save_CHEMICAL_CONN_ATOM save_chemical_conn_atom.charge save_chemical_conn_atom.display_x save_chemical_conn_atom.display_y save_chemical_conn_atom.NCA save_chemical_conn_atom.NH save_chemical_conn_atom.number save_chemical_conn_atom.type_symbol save_CHEMICAL_CONN_BOND save_chemical_conn_bond.atom_1 save_chemical_conn_bond.atom_2 save_chemical_conn_bond.type save_CHEMICAL_FORMULA save_chemical_formula.analytical save_chemical_formula.block_id save_chemical_formula.moiety save_chemical_formula.structural save_chemical_formula.sum save_chemical_formula.weight save_chemical_formula.weight_meas save_CITATION save_citation.abstract save_citation.book_coden_ISBN save_citation.book_publisher save_citation.book_title save_citation.coordinate_linkage save_citation.country save_citation.details save_citation.id save_citation.journal_abbrev save_citation.journal_coden_ASTM save_citation.journal_coden_ISSN save_citation.journal_coden_PDB save_citation.journal_full save_citation.journal_issue save_citation.journal_volume save_citation.language save_citation.Medline_AN save_citation.page_first save_citation.page_last save_citation.title save_citation.year save_CITATION_AUTHOR save_citation_author.citation_id save_citation_author.name save_CITATION_EDITOR save_citation_editor.citation_id save_citation_editor.name save_COMP_PROG save_comp_prog.citation_id save_comp_prog.name save_comp_prog.task save_comp_prog.version save_COMPUTING save_computing.block_id save_computing.cell_refinement save_computing.data_collection save_computing.data_reduction save_computing.molecular_graphics save_computing.publication_material save_computing.structure_refinement save_computing.structure_solution save_DATABASE save_database.block_id save_database.code_CAS save_database.code_CSD save_database.code_ICSD save_database.code_MDF save_database.code_NBS save_database.code_PDF save_database.journal_ASTM save_database.journal_CSD save_DATABASE_NEW save_database_new.database_id save_database_new.database_code save_DATABASE_PDB_REMARK save_database_PDB_remark.num save_database_PDB_remark.text save_DATABASE_PDB_REV save_database_PDB_rev.author_name save_database_PDB_rev.date save_database_PDB_rev.date_original save_database_PDB_rev.mod_type save_database_PDB_rev.num save_database_PDB_rev.replaced_by save_database_PDB_rev.replaces save_database_PDB_rev.status save_DATABASE_PDB_REV_RECORD save_database_PDB_rev_record.details save_database_PDB_rev_record.rev_num save_database_PDB_rev_record.type save_DIFFRN save_diffrn.ambient_environment save_diffrn.ambient_pressure save_diffrn.ambient_pressure_esd save_diffrn.ambient_temperature save_diffrn.ambient_temperature_esd save_diffrn.block_id save_diffrn.crystal_support save_diffrn.crystal_treatment save_diffrn.details save_DIFFRN_ATTENUATOR save_diffrn_attenuator.code save_diffrn_attenuator.scale save_DIFFRN_MEASUREMENT save_diffrn_measurement.block_id save_diffrn_measurement.details save_diffrn_measurement.device save_diffrn_measurement.device_details save_diffrn_measurement.device_specific save_diffrn_measurement.device_type save_diffrn_measurement.method save_DIFFRN_ORIENT_MATRIX save_diffrn_orient_matrix.block_id save_diffrn_orient_matrix.type save_diffrn_orient_matrix.UB save_diffrn_orient_matrix.UB[1][1] save_diffrn_orient_matrix.UB[1][2] save_diffrn_orient_matrix.UB[1][3] save_diffrn_orient_matrix.UB[2][1] save_diffrn_orient_matrix.UB[2][2] save_diffrn_orient_matrix.UB[2][3] save_diffrn_orient_matrix.UB[3][1] save_diffrn_orient_matrix.UB[3][2] save_diffrn_orient_matrix.UB[3][3] save_DIFFRN_ORIENT_REFLN save_diffrn_orient_refln.angle_chi save_diffrn_orient_refln.angle_kappa save_diffrn_orient_refln.angle_phi save_diffrn_orient_refln.angle_psi save_diffrn_orient_refln.index_h save_diffrn_orient_refln.index_k save_diffrn_orient_refln.index_l save_DIFFRN_RADIATION save_diffrn_radiation.block_id save_diffrn_radiation.collimation save_diffrn_radiation.detector save_diffrn_radiation_detector_details save_diffrn_radiation.detector_dtime save_diffrn_radiation.detector_specific save_diffrn_radiation.detector_type save_diffrn_radiation.filter_edge save_diffrn_radiation.inhomogeneity save_diffrn_radiation.monochromator save_diffrn_radiation.polarisn_norm save_diffrn_radiation.polarisn_ratio save_diffrn_radiation.source save_diffrn_radiation.source_details save_diffrn_radiation.source_power save_diffrn_radiation.source_specific save_diffrn_radiation.source_target save_diffrn_radiation.source_type save_diffrn_radiation.type save_diffrn_radiation.wavelength save_diffrn_radiation.wavelength_id save_diffrn_radiation.wavelength_wt save_DIFFRN_REFLN save_diffrn_refln.angle_chi save_diffrn_refln.angle_kappa save_diffrn_refln.angle_omega save_diffrn_refln.angle_phi save_diffrn_refln.angle_psi save_diffrn_refln.angle_theta save_diffrn_refln.attenuator_code save_diffrn_refln.counts_bg_1 save_diffrn_refln.counts_bg_2 save_diffrn_refln.counts_net save_diffrn_refln.counts_peak save_diffrn_refln.counts_total save_diffrn_refln.crystal_id save_diffrn_refln.detect_slit_horiz save_diffrn_refln.detect_slit_vert save_diffrn_refln.elapsed_time save_diffrn_refln.id save_diffrn_refln.index_h save_diffrn_refln.index_k save_diffrn_refln.index_l save_diffrn_refln.intensity_net save_diffrn_refln.intensity_sigma save_diffrn_refln.scale_group_code save_diffrn_refln.scan_mode save_diffrn_refln.scan_mode_backgd save_diffrn_refln.scan_width save_diffrn_refln.sint/lambda save_diffrn_refln.standard_code save_diffrn_refln.wavelength save_diffrn_refln.wavelength_id save_DIFFRN_REFLNS save_diffrn_reflns.av_R_equivalents save_diffrn_reflns.av_sigmaI/netI save_diffrn_reflns.block_id save_diffrn_reflns.limit_h_max save_diffrn_reflns.limit_h_min save_diffrn_reflns.limit_k_max save_diffrn_reflns.limit_k_min save_diffrn_reflns.limit_l_max save_diffrn_reflns.limit_l_min save_diffrn_reflns.number save_diffrn_reflns.reduction_process save_diffrn_reflns.theta_max save_diffrn_reflns.theta_min save_diffrn_reflns.transf_matrix save_diffrn_reflns.transf_matrix[1][1] save_diffrn_reflns.transf_matrix[1][2] save_diffrn_reflns.transf_matrix[1][3] save_diffrn_reflns.transf_matrix[2][1] save_diffrn_reflns.transf_matrix[2][2] save_diffrn_reflns.transf_matrix[2][3] save_diffrn_reflns.transf_matrix[3][1] save_diffrn_reflns.transf_matrix[3][2] save_diffrn_reflns.transf_matrix[3][3] save_DIFFRN_SCALE_GROUP save_diffrn_scale_group.code save_diffrn_scale_group.I_net save_DIFFRN_STANDARD_REFLN save_diffrn_standard_refln.code save_diffrn_standard_refln.index_h save_diffrn_standard_refln.index_k save_diffrn_standard_refln.index_l save_DIFFRN_STANDARDS save_diffrn_standards.block_id save_diffrn_standards.decay_ save_diffrn_standards.interval_count save_diffrn_standards.interval_time save_diffrn_standards.number save_diffrn_standards.scale_sigma save_ENTITY save_entity.details save_entity.formula_weight save_entity.id save_entity.src_method save_entity.type save_ENTITY_KEYWORDS save_entity_keywords.entity_id save_entity_keywords.text save_ENTITY_LINK save_entity_link.id save_entity_link.details save_entity_link.type_mon_1 save_entity_link.type_mon_2 save_ENTITY_LINK_ANGLE save_entity_link_angle.atom_1_atom_id save_entity_link_angle.atom_1_mon_id save_entity_link_angle.atom_2_atom_id save_entity_link_angle.atom_2_mon_id save_entity_link_angle.atom_3_atom_id save_entity_link_angle.atom_3_mon_id save_entity_link_angle.value_angle save_entity_link_angle.value_angle_esd save_entity_link_angle.value_dist save_entity_link_angle.value_dist_esd save_ENTITY_LINK_BOND save_entity_link_bond.atom_1_atom_id save_entity_link_bond.atom_1_mon_id save_entity_link_bond.atom_2_atom_id save_entity_link_bond.atom_2_mon_id save_entity_link_bond.value_order save_entity_link_bond.value_dist save_entity_link_bond.value_dist_esd save_ENTITY_MON save_entity_mon.id save_entity_mon.model_details save_entity_mon.model_erf save_entity_mon.model_source save_entity_mon.name save_entity_mon.nstd_class save_entity_mon.nstd_details save_entity_mon.nstd_flag save_entity_mon.nstd_parent save_entity_mon.number_atoms_all save_entity_mon.number_atoms_nh save_entity_mon.one_letter_code save_entity_mon.type save_ENTITY_MON_ANGLE save_entity_mon_angle.atom_id_1 save_entity_mon_angle.atom_id_2 save_entity_mon_angle.atom_id_3 save_entity_mon_angle.mon_id save_entity_mon_angle.value_angle save_entity_mon_angle.value_angle_esd save_entity_mon_angle.value_dist save_entity_mon_angle.value_dist_esd save_ENTITY_MON_ATOM save_entity_mon_atom.alt_atom_id save_entity_mon_atom.atom_id save_entity_mon_atom.charge save_entity_mon_atom.model_cartn_x save_entity_mon_atom.model_cartn_x_esd save_entity_mon_atom.model_cartn_y save_entity_mon_atom.model_cartn_y_esd save_entity_mon_atom.model_cartn_z save_entity_mon_atom.model_cartn_z_esd save_entity_mon_atom.mon_id save_entity_mon_atom.substruct_code save_entity_mon_atom.type_symbol save_ENTITY_MON_BOND save_entity_mon_bond.atom_id_1 save_entity_mon_bond.atom_id_2 save_entity_mon_bond.mon_id save_entity_mon_bond.value_order save_entity_mon_bond.value_dist save_entity_mon_bond.value_dist_esd save_ENTITY_MON_CHIR save_entity_mon_chir.atom_id save_entity_mon_chir.id save_entity_mon_chir.mon_id save_entity_mon_chir.number_atoms_all save_entity_mon_chir.number_atoms_nh save_entity_mon_chir.volume_flag save_entity_mon_chir.volume_three save_entity_mon_chir.volume_three_esd save_ENTITY_MON_CHIR_ATOM save_entity_mon_chir_atom.atom_id save_entity_mon_chir_atom.chir_id save_entity_mon_chir_atom.dev save_ENTITY_MON_PLANE save_entity_mon_plane.id save_entity_mon_plane.mon_id save_entity_mon_plane.number_atoms_all save_entity_mon_plane.number_atoms_nh save_ENTITY_MON_PLANE_ATOM save_entity_mon_plane_atom.atom_id save_entity_mon_plane_atom.plane_id save_ENTITY_MON_TOR save_entity_mon_tor.atom_id_1 save_entity_mon_tor.atom_id_2 save_entity_mon_tor.atom_id_3 save_entity_mon_tor.atom_id_4 save_entity_mon_tor.id save_entity_mon_tor.mon_id save_ENTITY_MON_TOR_VALUE save_entity_mon_tor_value.tor_id save_entity_mon_tor_value.angle save_entity_mon_tor_value.angle_esd save_entity_mon_tor_value.dist save_entity_mon_tor_value.dist_esd save_ENTITY_NAME_COM save_entity_name_com.entity_id save_entity_name_com.name save_ENTITY_NAME_SYS save_entity_name_sys.entity_id save_entity_name_sys.name save_entity_name_sys.system save_ENTITY_POLY save_entity_poly.entity_id save_entity_poly.nstd_chirality save_entity_poly.nstd_linkage save_entity_poly.nstd_monomer save_entity_poly.number_of_monomers save_entity_poly.type save_entity_poly.type_details save_ENTITY_POLY_SEQ save_entity_poly_seq.entity_id save_entity_poly_seq.hetero save_entity_poly_seq.mon_id save_entity_poly_seq.num save_ENTITY_POLY_SEQ_DIF save_entity_poly_seq_dif.db_mon_id save_entity_poly_seq_dif.db_code save_entity_poly_seq_dif.db_name save_entity_poly_seq_dif.details save_entity_poly_seq_dif.entity_id save_entity_poly_seq_dif.mon_id save_entity_poly_seq_dif.seq_num save_ENTITY_REFERENCE save_entity_reference.database_code save_entity_reference.database_name save_entity_reference.details save_entity_reference.entity_id save_ENTITY_SRC_GEN save_entity_src_gen.entity_id save_entity_src_gen.gene_src_common_name save_entity_src_gen.gene_src_details save_entity_src_gen.gene_src_genus save_entity_src_gen.gene_src_species save_entity_src_gen.gene_src_strain save_entity_src_gen.gene_src_tissue save_entity_src_gen.gene_src_tissue_fraction save_entity_src_gen.host_org_common_name save_entity_src_gen.host_org_details save_entity_src_gen.host_org_genus save_entity_src_gen.host_org_species save_entity_src_gen.host_org_strain save_entity_src_gen.plasmid_details save_entity_src_gen.plasmid_name save_ENTITY_SRC_NAT save_entity_src_nat.common_name save_entity_src_nat.details save_entity_src_nat.entity_id save_entity_src_nat.genus save_entity_src_nat.species save_entity_src_nat.strain save_entity_src_nat.tissue save_entity_src_nat.tissue_fraction save_EXPTL save_exptl.absorpt_coefficient_mu save_exptl.absorpt_correction_T_max save_exptl.absorpt_correction_T_min save_exptl.absorpt_correction_type save_exptl.absorpt_process_details save_exptl.block_id save_exptl.crystals_number save_exptl.details save_EXPTL_CRYSTAL save_exptl_crystal.colour save_exptl_crystal.density_diffrn save_exptl_crystal.density_meas save_exptl_crystal.density_meas_temp save_exptl_crystal.density_method save_exptl_crystal.density_percent_sol save_exptl_crystal.description save_exptl_crystal.F_000 save_exptl_crystal.id save_exptl_crystal.preparation save_exptl_crystal.size_max save_exptl_crystal.size_mid save_exptl_crystal.size_min save_exptl_crystal.size_rad save_EXPTL_CRYSTAL_FACE save_exptl_crystal_face.diffr_chi save_exptl_crystal_face.diffr_kappa save_exptl_crystal_face.diffr_phi save_exptl_crystal_face.diffr_psi save_exptl_crystal_face.index_h save_exptl_crystal_face.index_k save_exptl_crystal_face.index_l save_exptl_crystal_face.perp_dist save_EXPTL_CRYSTAL_GROW save_exptl_crystal_grow.apparatus save_exptl_crystal_grow.atmosphere save_exptl_crystal_grow.crystal_id save_exptl_crystal_grow.details save_exptl_crystal_grow.method save_exptl_crystal_grow.method_ref save_exptl_crystal_grow.pH save_exptl_crystal_grow.pressure save_exptl_crystal_grow.pressure_esd save_exptl_crystal_grow.seeding save_exptl_crystal_grow.seeding_ref save_exptl_crystal_grow.temp save_exptl_crystal_grow.temp_esd save_exptl_crystal_grow.time save_EXPTL_CRYSTAL_GROW_COMP save_exptl_crystal_grow_comp.conc save_exptl_crystal_grow_comp.details save_exptl_crystal_grow_comp.id save_exptl_crystal_grow_comp.name save_exptl_crystal_grow_comp.sol_id save_exptl_crystal_grow_comp.volume save_GEOM save_geom.block_id save_geom.details save_GEOM_ANGLE save_geom_angle.value save_geom_angle.value_esd save_geom_angle.atom_site_label_1 save_geom_angle.atom_site_label_2 save_geom_angle.atom_site_label_3 save_geom_angle.publ_flag save_geom_angle.site_symmetry_1 save_geom_angle.site_symmetry_2 save_geom_angle.site_symmetry_3 save_GEOM_BOND save_geom_bond.atom_site_label_1 save_geom_bond.atom_site_label_2 save_geom_bond.distance save_geom_bond.distance_esd save_geom_bond.publ_flag save_geom_bond.site_symmetry_1 save_geom_bond.site_symmetry_2 save_GEOM_CONTACT save_geom_contact.atom_site_label_1 save_geom_contact.atom_site_label_2 save_geom_contact.distance save_geom_contact.distance save_geom_contact.publ_flag save_geom_contact.site_symmetry_1 save_geom_contact.site_symmetry_2 save_GEOM_TORSION save_geom_torsion.value save_geom_torsion.value_esd save_geom_torsion.atom_site_label_1 save_geom_torsion.atom_site_label_2 save_geom_torsion.atom_site_label_3 save_geom_torsion.atom_site_label_4 save_geom_torsion.publ_flag save_geom_torsion.site_symmetry_1 save_geom_torsion.site_symmetry_2 save_geom_torsion.site_symmetry_3 save_geom_torsion.site_symmetry_4 save_JOURNAL save_journal.block_id save_journal.coden_ASTM save_journal.coden_Cambridge save_journal.coeditor_address save_journal.coeditor_code save_journal.coeditor_email save_journal.coeditor_fax save_journal.coeditor_name save_journal.coeditor_notes save_journal.coeditor_phone save_journal.date_accepted save_journal.date_from_coeditor save_journal.date_to_coeditor save_journal.date_printers_final save_journal.date_printers_first save_journal.date_proofs_in save_journal.date_proofs_out save_journal.date_recd_copyright save_journal.date_recd_electronic save_journal.date_recd_hard_copy save_journal.issue save_journal.name_full save_journal.page_first save_journal.page_last save_journal.suppl_publ_number save_journal.suppl_publ_pages save_journal.techeditor_address save_journal.techeditor_code save_journal.techeditor_email save_journal.techeditor_fax save_journal.techeditor_name save_journal.techeditor_notes save_journal.techeditor_phone save_journal.volume save_journal.year save_PHASING save_phasing.method save_PHASING_AVERAGING save_phasing_averaging.block_id save_phasing_averaging.details save_phasing_averaging.method save_PHASING_ISOMORPHOUS save_phasing_isomorphous.block_id save_phasing_isomorphous.details save_phasing_isomorphous.method save_phasing_isomorphous.parent save_PHASING_MAD save_phasing_MAD.block_id save_phasing_MAD.details save_phasing_MAD.method save_PHASING_MIR save_phasing_MIR.block_id save_phasing_MIR.details save_phasing_MIR.method save_PHASING_MIR_DER save_phasing_MIR_der.details save_phasing_MIR_der.id save_phasing_MIR_der.number_of_sites save_phasing_MIR_der.reflns_criteria save_PHASING_MIR_DER_SHELL save_phasing_MIR_der_shell.d_res_high save_phasing_MIR_der_shell.d_res_low save_phasing_MIR_der_shell.der_id save_phasing_MIR_der_shell.fom save_phasing_MIR_der_shell.ha_ampl save_phasing_MIR_der_shell.loc save_phasing_MIR_der_shell.phase save_phasing_MIR_der_shell.power save_phasing_MIR_der_shell.R_Cullis save_phasing_MIR_der_shell.R_Kraut save_phasing_MIR_der_shell.reflns save_PHASING_MIR_REFLN save_phasing_MIR_refln.A_calc save_phasing_MIR_refln.A_meas save_phasing_MIR_refln.B_calc save_phasing_MIR_refln.B_meas save_phasing_MIR_refln.der_id save_phasing_MIR_refln.F_calc save_phasing_MIR_refln.F_meas save_phasing_MIR_refln.F_sigma save_phasing_MIR_refln.HL_A_iso save_phasing_MIR_refln.HL_B_iso save_phasing_MIR_refln.HL_C_iso save_phasing_MIR_refln.HL_D_iso save_phasing_MIR_refln.index_h save_phasing_MIR_refln.index_k save_phasing_MIR_refln.index_l save_phasing_MIR_refln.phase_calc save_phasing_MIR_refln.phase_meas save_PHASING_MIR_SHELL save_phasing_MIR_shell.d_res_high save_phasing_MIR_shell.d_res_low save_phasing_MIR_shell.fom save_phasing_MIR_shell.loc save_phasing_MIR_shell.mean_phase save_phasing_MIR_shell.power save_phasing_MIR_shell.R_Cullis save_phasing_MIR_shell.R_Kraut save_phasing_MIR_shell.reflns save_PHASING_MIR_SITE save_phasing_MIR_site.atom_type_symbol save_phasing_MIR_site.B_iso save_phasing_MIR_site.B_iso_esd save_phasing_MIR_site.cartn_x save_phasing_MIR_site.cartn_x_esd save_phasing_MIR_site.cartn_y save_phasing_MIR_site.cartn_y_esd save_phasing_MIR_site.cartn_z save_phasing_MIR_site.cartn_z_esd save_phasing_MIR_site.der_id save_phasing_MIR_site.details save_phasing_MIR_site.fract_x save_phasing_MIR_site.fract_x_esd save_phasing_MIR_site.fract_y save_phasing_MIR_site.fract_y_esd save_phasing_MIR_site.fract_z save_phasing_MIR_site.fract_z_esd save_phasing_MIR_site.id save_phasing_MIR_site.occupancy save_PHASING_MR save_phasing_MR.block_id save_phasing_MR.method save_PUBL save_publ.block_id save_publ.contact_author save_publ.contact_author_email save_publ.contact_author_fax save_publ.contact_author_phone save_publ.contact_letter save_publ.manuscript_creation save_publ.manuscript_processed save_publ.manuscript_text save_publ.requested_coeditor_name save_publ.requested_journal save_publ.section_abstract save_publ.section_acknowledgements save_publ.section_comment save_publ.section_discussion save_publ.section_experimental save_publ.section_exptl_prep save_publ.section_exptl_refinement save_publ.section_figure_captions save_publ.section_introduction save_publ.section_references save_publ.section_table_legends save_publ.section_title save_PUBL_AUTHOR save_publ_author.address save_publ_author.name save_PUBL_MANUSCRIPT_INCL save_publ_manuscript_incl.block_id save_publ_manuscript_incl.extra_item save_publ_manuscript_incl.extra_info save_publ_manuscript_incl.extra_defn save_REFINE_HIST save_refine_hist.cycle_id save_refine_hist.details save_refine_hist.d_res_high save_refine_hist.d_res_low save_refine_hist.number_atoms_solvent save_refine_hist.number_atoms_total save_refine_hist.number_reflns_obs save_refine_hist.R_factor_obs save_REFINE save_refine.block_id save_refine.details save_refine.diff_density_max save_refine.diff_density_max_esd save_refine.diff_density_min save_refine.diff_density_min_esd save_refine.diff_density_rms save_refine.diff_density_rms_esd save_refine.B_iso_max save_refine.B_iso_min save_refine.ls_abs_structure_details save_refine.ls_abs_structure_Flack save_refine.ls_abs_structure_Flack_esd save_refine.ls_abs_structure_Rogers save_refine.ls_abs_structure_Rogers_esd save_refine.ls_extinction_coef save_refine.ls_extinction_coef_esd save_refine.ls_extinction_expression save_refine.ls_extinction_method save_refine.ls_goodness_of_fit_all save_refine.ls_goodness_of_fit_all_esd save_refine.ls_goodness_of_fit_obs save_refine.ls_goodness_of_fit_obs_esd save_refine.ls_hydrogen_treatment save_refine.ls_matrix_type save_refine.ls_number_constraints save_refine.ls_number_parameters save_refine.ls_number_reflns_all save_refine.ls_number_reflns_obs save_refine_ls.number_reflns_R_free save_refine.ls_number_restraints save_refine.ls_R_factor_all save_refine.ls_R_factor_obs save_refine.ls_R_factor_R_free save_refine.ls_restrained_S_all save_refine.ls_restrained_S_obs save_refine.ls_shift/esd_max save_refine.ls_shift/esd_mean save_refine.ls_structure_factor_coef save_refine.ls_weighting_details save_refine.ls_weighting_scheme save_refine.ls_wR_factor_all save_refine.ls_wR_factor_obs save_refine.ls_wR_factor_R_free save_refine.occupancy_max save_refine.occupancy_min save_REFINE_B_ISO save_refine_b_iso.class save_refine_b_iso.details save_refine_b_iso.treatment save_refine_b_iso.value save_REFINE_LS_RESTR save_refine_ls_restr.criterion save_refine_ls_restr.dev_ideal save_refine_ls_restr.number save_refine_ls_restr.rejects save_refine_ls_restr.dev_ideal_target save_refine_ls_restr.type save_REFINE_LS_SHELL save_refine_ls_shell.number_reflns_all save_refine_ls_shell.number_reflns_obs save_refine_ls_shell.number_reflns_R_free save_refine_ls_shell.d_res_high save_refine_ls_shell.d_res_low save_refine_ls_shell.R_factor_all save_refine_ls_shell.R_factor_obs save_refine_ls_shell.R_factor_R_free save_refine_ls_shell.wR_factor_all save_refine_ls_shell.wR_factor_obs save_refine_ls_shell.wR_factor_R_free save_REFINE_OCCUPANCY save_refine_occupancy.class save_refine_occupancy.details save_refine_occupancy.treatment save_refine_occupancy.value save_REFLN save_refln.A_calc save_refln.A_meas save_refln.B_calc save_refln.B_meas save_refln.crystal_id save_refln.F_calc save_refln.F_meas save_refln.F_sigma save_refln.F_squared_calc save_refln.F_squared_meas save_refln.F_squared_sigma save_refln.HL_coeff_A save_refln.index_h save_refln.index_k save_refln.index_l save_refln.intensity_calc save_refln.intensity_meas save_refln.intensity_sigma save_refln.mean_path_length_tbar save_refln.status save_refln.phase_calc save_refln.phase_meas save_refln.refinement_status save_refln.scale_group_code save_refln.sint/lambda save_refln.symmetry_epsilon save_refln.symmetry_multiplicity save_refln.wavelength save_refln.wavelength_id save_REFLNS save_reflns.block_id save_reflns.data_reduction_details save_reflns.data_reduction_method save_reflns.d_resolution_high save_reflns.d_resolution_low save_reflns.details save_reflns.limit_h_max save_reflns.limit_h_min save_reflns.limit_k_max save_reflns.limit_k_min save_reflns.limit_l_max save_reflns.limit_l_min save_reflns.number_all save_reflns.number_obs save_reflns.observed_criterion save_reflns.R_free_details save_REFLNS_SCALE save_reflns_scale.group_code save_reflns_scale.meas_F save_reflns_scale.meas_F_squared save_reflns_scale.meas_intensity save_REFLNS_SHELL save_reflns_shell.number_measured_all save_reflns_shell.number_measured_obs save_reflns_shell.number_possible save_reflns_shell.number_unique_all save_reflns_shell.number_unique_obs save_reflns_shell.d_res_high save_reflns_shell.d_res_low save_reflns_shell.meanI/sigI_all save_reflns_shell.meanI/sigI_obs save_reflns_shell.percent_possible_all save_reflns_shell.percent_possible_obs save_reflns_shell.Rmerge_F_all save_reflns_shell.Rmerge_F_obs save_reflns_shell.Rmerge_I_all save_reflns_shell.Rmerge_I_obs save_STRUCT save_struct.block_id save_struct.keywords save_struct.title save_STRUCT_ASYM save_struct_asym.details save_struct_asym.entity_id save_struct_asym.id save_STRUCT_BIOL save_struct_biol.details save_struct_biol.id save_STRUCT_BIOL_GEN save_struct_biol_gen.asym_id save_struct_biol_gen.biol_id save_struct_biol_gen.details save_struct_biol_gen.symmetry save_STRUCT_BIOL_KEYWORDS save_struct_biol_keywords.biol_id save_struct_biol_keywords.text save_STRUCT_BIOL_VIEW save_struct_biol_view.biol_id save_struct_biol_view.details save_struct_biol_view.id save_struct_biol_view.rot_matrix save_STRUCT_CONF save_struct_conf.beg_label_asym_id save_struct_conf.beg_label_res_id save_struct_conf.beg_label_seq_id save_struct_conf.conf_type_id save_struct_conf.details save_struct_conf.end_label_asym_id save_struct_conf.end_label_res_id save_struct_conf.end_label_seq_id save_struct_conf.id save_STRUCT_CONF_TYPE save_struct_conf_type.criteria save_struct_conf_type.id save_struct_conf_type.reference save_STRUCT_CONN save_struct_conn.conn_type_id save_struct_conn.details save_struct_conn.id save_struct_conn.ptnr1_label_alt_id save_struct_conn.ptnr1_label_asym_id save_struct_conn.ptnr1_label_atom_id save_struct_conn.ptnr1_label_res_id save_struct_conn.ptnr1_label_seq_id save_struct_conn.ptnr1_role save_struct_conn.ptnr1_symmetry save_struct_conn.ptnr2_label_alt_id save_struct_conn.ptnr2_label_asym_id save_struct_conn.ptnr2_label_atom_id save_struct_conn.ptnr2_label_res_id save_struct_conn.ptnr2_label_seq_id save_struct_conn.ptnr2_role save_struct_conn.ptnr2_symmetry save_STRUCT_CONN_TYPE save_struct_conn_type.criteria save_struct_conn_type.id save_struct_conn_type.reference save_STRUCT_MON_DETAILS save_struct_mon_details.block_id save_struct_mon_details.prot_cis save_struct_mon_details.RSCC save_struct_mon_details.RSR save_STRUCT_MON_NUCL save_struct_mon_nucl.alpha save_struct_mon_nucl.beta save_struct_mon_nucl.chi1 save_struct_mon_nucl.chi2 save_struct_mon_nucl.delta save_struct_mon_nucl.details save_struct_mon_nucl.epsilon save_struct_mon_nucl.gamma save_struct_mon_nucl.label_alt_id save_struct_mon_nucl.label_asym_id save_struct_mon_nucl.label_res_id save_struct_mon_nucl.label_seq_id save_struct_mon_nucl.mean_B_all save_struct_mon_nucl.mean_B_base save_struct_mon_nucl.mean_B_phos save_struct_mon_nucl.mean_B_sugar save_struct_mon_nucl.nu0 save_struct_mon_nucl.nu1 save_struct_mon_nucl.nu2 save_struct_mon_nucl.nu3 save_struct_mon_nucl.nu4 save_struct_mon_nucl.RSCC_all save_struct_mon_nucl.RSCC_base save_struct_mon_nucl.RSCC_phos save_struct_mon_nucl.RSCC_sugar save_struct_mon_nucl.RSR_all save_struct_mon_nucl.RSR_base save_struct_mon_nucl.RSR_phos save_struct_mon_nucl.RSR_sugar save_struct_mon_nucl.zeta save_STRUCT_MON_PROT save_struct_mon_prot.chi1 save_struct_mon_prot.chi2 save_struct_mon_prot.chi3 save_struct_mon_prot.chi4 save_struct_mon_prot.chi5 save_struct_mon_prot.details save_struct_mon_prot.label_alt_id save_struct_mon_prot.label_asym_id save_struct_mon_prot.label_res_id save_struct_mon_prot.label_seq_id save_struct_mon_prot.RSCC_all save_struct_mon_prot.RSCC_main save_struct_mon_prot.RSCC_side save_struct_mon_prot.RSR_all save_struct_mon_prot.RSR_main save_struct_mon_prot.RSR_side save_struct_mon_prot.mean_B_all save_struct_mon_prot.mean_B_main save_struct_mon_prot.mean_B_side save_struct_mon_prot.omega save_struct_mon_prot.phi save_struct_mon_prot.psi save_STRUCT_MON_CIS save_struct_mon_prot_cis.label_alt_id save_struct_mon_prot_cis.label_asym_id save_struct_mon_prot_cis.label_res_id save_struct_mon_prot_cis.label_seq_id save_STRUCT_NCS_DOM save_struct_ncs_dom.details save_struct_ncs_dom.id save_STRUCT_NCS_DOM_GEN save_struct_ncs_dom_gen.beg_label_alt_id save_struct_ncs_dom_gen.beg_label_asym_id save_struct_ncs_dom_gen.beg_label_res_id save_struct_ncs_dom_gen.beg_label_seq_id save_struct_ncs_dom_gen.dom_id save_struct_ncs_dom_gen.end_label_alt_id save_struct_ncs_dom_gen.end_label_asym_id save_struct_ncs_dom_gen.end_label_res_id save_struct_ncs_dom_gen.end_label_seq_id save_STRUCT_NCS_ENS save_struct_ncs_ens.details save_struct_ncs_ens.id save_struct_ncs_ens.point_group save_STRUCT_NCS_ENS_OPER save_struct_ncs_ens_oper.details save_struct_ncs_ens_oper.dom_id_1 save_struct_ncs_ens_oper.dom_id_2 save_struct_ncs_ens_oper.ens_id save_struct_ncs_ens_oper.kappa save_struct_ncs_ens_oper.phi save_struct_ncs_ens_oper.psi save_STRUCT_SITE save_struct_site.details save_struct_site.id save_STRUCT_SITE_GEN save_struct_site_gen.details save_struct_site_gen.id save_struct_site_gen.label_alt_id save_struct_site_gen.label_asym_id save_struct_site_gen.label_atom_id save_struct_site_gen.label_res_id save_struct_site_gen.label_seq_id save_struct_site_gen.site_id save_struct_site_gen.symmetry save_STRUCT_SITE_KEYWORDS save_struct_site_keywords.site_id save_struct_site_keywords.text save_STRUCT_SITE_VIEW save_struct_site_view.details save_struct_site_view.id save_struct_site_view.rot_matrix save_struct_site_view.site_id save_SYMMETRY save_symmetry.block_id save_symmetry.cell_setting save_symmetry.Int_Tables_number save_symmetry.space_group_name_Hall save_symmetry.space_group_name_H-M save_SYMMETRY_EQUIV save_symmetry_equiv.id save_symmetry_equiv.pos_as_xyz
_category.description ; Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions, and so on. The data items for describing anisotropic temperature or thermal displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. ; _category.id _category.id _category.mandatory_code no _category_key.name '_atom_site.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_site.group_PDB _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_res_id _atom_site.label_asym_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.cartn_x _atom_site.cartn_y _atom_site.cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.footnote_id _atom_site.entity_id _atom_site.entity_seq_num ATOM N N VAL A 11 . 25.369 30.691 11.795 1.00 17.93 . 1 11 ATOM C CA VAL A 11 . 25.970 31.965 12.332 1.00 17.75 . 1 11 ATOM C C VAL A 11 . 25.569 32.010 13.808 1.00 17.83 . 1 11 ATOM O O VAL A 11 . 24.735 31.190 14.167 1.00 17.53 . 1 11 ATOM C CB VAL A 11 . 25.379 33.146 11.540 1.00 17.66 . 1 11 ATOM C CG1 VAL A 11 . 25.584 33.034 10.030 1.00 18.86 . 1 11 ATOM C CG2 VAL A 11 . 23.933 33.309 11.872 1.00 17.12 . 1 11 ATOM N N THR A 12 . 26.095 32.930 14.590 1.00 18.97 4 1 12 ATOM C CA THR A 12 . 25.734 32.995 16.032 1.00 19.80 4 1 12 ATOM C C THR A 12 . 24.695 34.106 16.113 1.00 20.92 4 1 12 ATOM O O THR A 12 . 24.869 35.118 15.421 1.00 21.84 4 1 12 ATOM C CB THR A 12 . 26.911 33.346 17.018 1.00 20.51 4 1 12 ATOM O OG1 THR A 12 3 27.946 33.921 16.183 0.50 20.29 4 1 12 ATOM O OG1 THR A 12 4 27.769 32.142 17.103 0.50 20.59 4 1 12 ATOM C CG2 THR A 12 3 27.418 32.181 17.878 0.50 20.47 4 1 12 ATOM C CG2 THR A 12 4 26.489 33.778 18.426 0.50 20.00 4 1 12 ATOM N N ILE A 13 . 23.664 33.855 16.884 1.00 22.08 . 1 13 ATOM C CA ILE A 13 . 22.623 34.850 17.093 1.00 23.44 . 1 13 ATOM C C ILE A 13 . 22.657 35.113 18.610 1.00 25.77 . 1 13 ATOM O O ILE A 13 . 23.123 34.250 19.406 1.00 26.28 . 1 13 ATOM C CB ILE A 13 . 21.236 34.463 16.492 1.00 22.67 . 1 13 ATOM C CG1 ILE A 13 . 20.478 33.469 17.371 1.00 22.14 . 1 13 ATOM C CG2 ILE A 13 . 21.357 33.986 15.016 1.00 21.75 . 1 13 # - - - - data truncated for brevity - - - - ATOM C C1 APS C 300 1 4.171 29.012 7.116 0.58 17.27 1 2 . ATOM C C2 APS C 300 1 4.949 27.758 6.793 0.58 16.95 1 2 . ATOM O O3 APS C 300 1 4.800 26.678 7.393 0.58 16.85 1 2 . ATOM N N4 APS C 300 1 5.930 27.841 5.869 0.58 16.43 1 2 . # - - - - data truncated for brevity - - - - ;
_item_description.description ; These are the standard anisotropic atomic displacement components which appear in the structure factor term: exp(-1/4 sum~i~ sum~j~ B~ij~ h~i~ h~j~ a*~i~ a*~j~). The unique components of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_B' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U' 'constant' '_atom_site_anisotrop.U' 'constant' '_atom_site.aniso_U' 'alternative_exclusive' '_atom_site_anisotrop.B' 'alternative_exclusive' '_atom_site_anisotrop.U' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The estimated standard deviation of _atom_site.aniso_B. ; _item.name '_atom_site.aniso_B_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U_esd' 'constant' '_atom_site_anisotrop.U_esd' 'constant' '_atom_site.aniso_U_esd' 'alternative_exclusive' '_atom_site_anisotrop.B_esd' 'alternative_exclusive' '_atom_site_anisotrop.U_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
_item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site.aniso_ratio' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.ratio' 'alternative_exclusive' _item_range.maximum ? _item_range.minimum 1.0 _item_type.code float
_item_description.description ; These are the standard anisotropic atomic displacement components which appear in the structure factor term: exp(-2pi^2^ sum~i~ sum~j~ U~ij~ h~i~ h~j~ a*~i~ a*~j~). The unique components of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B' 'constant' '_atom_site_anisotrop.B' 'constant' '_atom_site.aniso_B' 'alternative_exclusive' '_atom_site_anisotrop.B' 'alternative_exclusive' '_atom_site_anisotrop.U' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The U[1][1] standard anisotropic atomic displacement component. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_site.aniso_U[1][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_11' _item_default.value 0.0 _item_related.related_name '_atom_site.aniso_U' _item_related.function_code 'alternative_exclusive' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The U[1][2] standard anisotropic atomic displacement component. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_site.aniso_U[1][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_12' _item_default.value 0.0 _item_related.related_name '_atom_site.aniso_U' _item_related.function_code 'alternative_exclusive' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The U[1][3] standard anisotropic atomic displacement component. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_site.aniso_U[1][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_13' _item_default.value 0.0 _item_related.related_name '_atom_site.aniso_U' _item_related.function_code 'alternative_exclusive' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The U[2][2] standard anisotropic atomic displacement component. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_site.aniso_U[2][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_22' _item_default.value 0.0 _item_related.related_name '_atom_site.aniso_U' _item_related.function_code 'alternative_exclusive' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The U[2][3] standard anisotropic atomic displacement component. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_site.aniso_U[2][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_23' _item_default.value 0.0 _item_related.related_name '_atom_site.aniso_U' _item_related.function_code 'alternative_exclusive' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The U[3][3] standard anisotropic atomic displacement component. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_site.aniso_U[3][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_33' _item_default.value 0.0 _item_related.related_name '_atom_site.aniso_U' _item_related.function_code 'alternative_exclusive' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
_item_description.description ; The estimated standard deviation of _atom_site.aniso_U. ; _item.name '_atom_site.aniso_U_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B_esd' 'constant' '_atom_site_anisotrop.B_esd' 'constant' '_atom_site.aniso_B_esd' 'alternative_exclusive' '_atom_site_anisotrop.B_esd' 'alternative_exclusive' '_atom_site_anisotrop.U_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site.attached_hydrogens.
_item_description.description ; The number of hydrogen atoms attached to the atom at this site excluding any H atoms for which coordinates (measured or calculated) are given. ; _item.name '_atom_site.attached_hydrogens' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_attached_hydrogens' _item_default.value 0 _item_range.maximum 4 _item_range.minimum 0 _item_type.code int loop_ _item_examples.case _item_examples.detail 2 'water oxygen' 1 'hydroxyl oxygen' 4 'ammonium nitrogen'
save_atom_site.B_iso_or_equiv.
_item_description.description ; Isotropic temperature factor parameter, or equivalent isotropic temperature factor calculated from anisotropic temperature factor parameters. The latter must be calculated as B(equiv) = (1/3) sumi{sumj(Bij a*i a*j Ai.Aj)} where A are the real cell, a* the reciprocal cell lengths, and Bij = 8pi**2Uij (see Fischer R X and Tillmanns E, Acta Cryst. C44 (1988) 775-776). ; _item.name '_atom_site.B_iso_or_equiv' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_related.related_name '_atom_site.U_iso_or_equiv' _item_related.function_code constant _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
save_atom_site.B_iso_or_equiv_esd.
_item_description.description ; The estimated standard deviation of _atom_site.B_iso_or_equiv. ; _item.name '_atom_site.B_iso_or_equiv_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_atom_site.U_iso_or_equiv_esd' _item_related.function_code constant _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site.calc_attached_atom.
_item_description.description ; The _atom_site.label of the atom site to which the 'geometry- calculated' atom site is attached. ; _item.name '_atom_site.calc_attached_atom' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_attached_atom' _item_type.code char
_item_description.description ; A standard code to signal if the site data has been determined by diffraction data or calculated from the geometry of surrounding sites, or has been assigned dummy coordinates. The abbreviation 'c' may be used in place of 'calc'. ; _item.name '_atom_site.calc_flag' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_flag' _item_default.value d _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail d 'determined from diffraction measurements' calc 'calculated from molecular geometry' c 'abbreviation for "calc"' dum 'dummy site with meaningless coordinates'
_item_description.description ; The x coordinate of the atom site position specified as orthogonal Angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.cartn_transform_axes. ; _item.name '_atom_site.cartn_x' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' _item_aliases.alias_name '_atom_site_cartn_x' loop_ _item_dependent.dependent_name '_atom_site.cartn_y' '_atom_site.cartn_z' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _atom_site.cartn_x. ; _item.name '_atom_site.cartn_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.cartn_y_esd' '_atom_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; The y coordinate of the atom site position specified as orthogonal Angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.cartn_transform_axes. ; _item.name '_atom_site.cartn_y' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' _item_aliases.alias_name '_atom_site_cartn_y' loop_ _item_dependent.dependent_name '_atom_site.cartn_x' '_atom_site.cartn_z' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _atom_site.cartn_y. ; _item.name '_atom_site.cartn_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.cartn_x_esd' '_atom_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; The z coordinate of the atom site position specified as orthogonal Angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.cartn_transform_axes. ; _item.name '_atom_site.cartn_z' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' _item_aliases.alias_name '_atom_site_cartn_z' loop_ _item_dependent.dependent_name '_atom_site.cartn_x' '_atom_site.cartn_y' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _atom_site.cartn_z. ; _item.name '_atom_site.cartn_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.cartn_x_esd' '_atom_site.cartn_y_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine_ls_number_constraints. ; _item.name '_atom_site.constraints' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_constraints' _item_default.value '.' _item_type.code char _item_examples.case 'pop=1.0-pop(Zn3)'
_item_description.description ; A description of special aspects of this site. See also _atom_site.refinement_flags. ; _item.name '_atom_site.description' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_description' _item_type.code char _item_examples.case 'Ag/Si disordered'
save_atom_site.disorder_group.
_item_description.description ; A code to link disordered atom sites of a group that exist simultaneously in the crystal structure. ; _item.name '_atom_site.disorder_group' _item.category_id _item.category_id _item.mandatory_code no _item_default.value '.' _item_type.code char _item_examples.case 'A'
_item_description.description ; The x coordinate of the atom site position specified as a fraction of _cell.length_a. ; _item.name '_atom_site.fract_x' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate' _item_aliases.alias_name '_atom_site_fract_x' loop_ _item_dependent.dependent_name '_atom_site.fract_y' '_atom_site.fract_z' _item_type.code float _item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.fract_x. ; _item.name '_atom_site.fract_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_y_esd' '_atom_site.fract_z_esd' _item_type.code float
_item_description.description ; The y coordinate of the atom site position specified as a fraction of _cell.length_b. ; _item.name '_atom_site.fract_y' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate' _item_aliases.alias_name '_atom_site_fract_y' loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_z' _item_type.code float _item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.fract_y. ; _item.name '_atom_site.fract_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_z_esd' _item_type.code float
_item_description.description ; The z coordinate of the atom site position specified as a fraction of _cell.length_c. ; _item.name '_atom_site.fract_z' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate' _item_aliases.alias_name '_atom_site_fract_z' loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_y' _item_type.code float _item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.fract_z. ; _item.name '_atom_site.fract_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item.sub_category_id 'fractional_coordinate_esd' loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_y_esd' _item_type.code float
_item_description.description ; The group of atoms to which the _atom_site. belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; _item.name '_atom_site.group_PDB' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value ATOM HETATM
_item_description.description ; The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. For compatibility with older files, _atom_site.label is aliases to _atom_site.id. ; _item.name '_atom_site.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
_item_description.description ; The _atom_site.label is a unique identifier for a particular site in the crystal. This code is made up of a sequence of up to seven components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.label' atom_site yes '_atom_site_anisotrop.label' atom_site_anisotrop yes '_geom_angle.atom_site_label_1' geom_angle yes '_geom_angle.atom_site_label_2' geom_angle yes '_geom_angle.atom_site_label_3' geom_angle yes '_geom_bond.atom_site_label_1' geom_bond yes '_geom_bond.atom_site_label_2' geom_bond yes '_geom_contact.atom_site_label_1' geom_contact yes '_geom_contact.atom_site_label_2' geom_contact yes '_geom_torsion.atom_site_label_1' geom_torsion yes '_geom_torsion.atom_site_label_2' geom_torsion yes '_geom_torsion.atom_site_label_3' geom_torsion yes '_geom_torsion.atom_site_label_4' geom_torsion yes loop_ _item_aliases.alias_name '_atom_site_label' '_atom_site.id' loop_ _item_linked.child_name _item_linked.parent_name '_atom_site_anisotrop.label' '_atom_site.label' '_geom_angle.atom_site_label_1' '_atom_site.label' '_geom_angle.atom_site_label_2' '_atom_site.label' '_geom_angle.atom_site_label_3' '_atom_site.label' '_geom_bond.atom_site_label_1' '_atom_site.label' '_geom_bond.atom_site_label_2' '_atom_site.label' '_geom_contact.atom_site_label_1' '_atom_site.label' '_geom_contact.atom_site_label_2' '_atom_site.label' '_geom_torsion.atom_site_label_1' '_atom_site.label' '_geom_torsion.atom_site_label_2' '_atom_site.label' '_geom_torsion.atom_site_label_3' '_atom_site.label' '_geom_torsion.atom_site_label_4' '_atom_site.label' _item_type.code char loop_ _item_examples.case C12 Ca3g28 Fe3+17 H*251 boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0
_item_description.description ; A component of the macromolecular identifier for this atom site. Note that this is not necessarily a number and does not have to correspond to the value of _atom_site.entity_seq_num. _atom_site.label_seq_id may be used for homology numbering, sequence numbering, and so on. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.label_seq_id' atom_site yes '_struct_conf.beg_label_seq_id' struct_conf yes '_struct_conf.end_label_seq_id' struct_conf yes '_struct_conn.ptnr1_label_seq_id' struct_conn yes '_struct_conn.ptnr2_label_seq_id' struct_conn yes '_struct_mon_nucl.label_seq_id' struct_mon_nucl yes '_struct_mon_prot.label_seq_id' struct_mon_prot yes '_struct_mon_prot_cis.label_seq_id' struct_mon_prot_cis yes '_struct_ncs_dom_gen.beg_label_seq_id' struct_ncs_dom_gen yes '_struct_ncs_dom_gen.end_label_seq_id' struct_ncs_dom_gen yes '_struct_site_gen.label_seq_id' struct_site_gen yes _item.sub_category_id 'mm_atom_site_label' loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_conf.end_label_seq_id' '_atom_site.label_seq_id' '_struct_conn.ptnr1_label_seq_id' '_atom_site.label_seq_id' '_struct_conn.ptnr2_label_seq_id' '_atom_site.label_seq_id' '_struct_mon_nucl.label_seq_id' '_atom_site.label_seq_id' '_struct_mon_prot.label_seq_id' '_atom_site.label_seq_id' '_struct_mon_prot_cis.label_seq_id' '_atom_site.label_seq_id' '_struct_ncs_dom_gen.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_ncs_dom_gen.end_label_seq_id' '_atom_site.label_seq_id' '_struct_site_gen.label_seq_id' '_atom_site.label_seq_id' _item_type.code char
_item_description.description ; The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. ; _item.name '_atom_site.occupancy' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_occupancy' _item_default.value 1.0 _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.occupancy. ; _item.name '_atom_site.occupancy_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_atom_site.refinement_flags.
_item_description.description ; A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. ; _item.name '_atom_site.refinement_flags' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_refinement_flags' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail . 'no refinement constraints' S 'special position constraint on site' G 'rigid group refinement of site' R ; riding atom site attached to non-riding atom ; D 'distance or angle restraint on site' T 'thermal displacement constraints' U 'Uiso or Uij restraint (rigid bond)' P 'partial occupancy constraint'
_item_description.description ; A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine_ls_number_restraints. ; _item.name '_atom_site.restraints' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_restraints' _item_type.code char _item_examples.case 'restrained to planar ring'
save_atom_site.symmetry_multiplicity.
_item_description.description ; The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography, Vol. A (1987). ; _item.name '_atom_site.symmetry_multiplicity' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_symmetry_multiplicity' _item_range.maximum 192 _item_range.minimum 1 _item_type.code int
save_atom_site.thermal_displace_type.
_item_description.description ; A standard code used to describe the type of atomic displacement parameters used for the site. ; _item.name '_atom_site.thermal_displace_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_thermal_displace_item_type' _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B'
save_atom_site.U_iso_or_equiv.
_item_description.description ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter calculated from anisotropic atomic displacement parameters. The latter must be calculated as U(equiv) = (1/3) sumi{sumj(Uij a*i a*j Ai.Aj)} where A are the real-cell and a* the reciprocal-cell lengths [see Fischer, R. X. and Tillmanns, E. (1988). Acta Cryst. C44, 775-776]. ; _item.name '_atom_site.U_iso_or_equiv' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_U_iso_or_equiv' _item_range.maximum 10.0 _item_range.minimum 0.0 _item_related.related_name '_atom_site.B_iso_or_equiv' _item_related.function_code constant _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
save_atom_site.U_iso_or_equiv_esd.
_item_description.description ; The estimated standard deviation of _atom_site.U_iso_or_equiv. ; _item.name '_atom_site.U_iso_or_equiv_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_atom_site.B_iso_or_equiv_esd' _item_related.function_code constant _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site.Wyckoff_symbol.
_item_description.description ; The Wyckoff symbol (letter) as listed in the space-group section of International Tables for Crystallography, Vol. A (1987). ; _item.name '_atom_site.Wyckoff_symbol' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_site_Wychkoff_symbol' _item_type.code char
_category.description ; Data items in the ATOM_SITE_ANISTROP category record details about temperature or thermal displacement factors, if those data items are contained in a separate list from the ATOM_SITE list. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. ; _category.id _category.id _category.mandatory_code no _category_key.name '_atom_site_anisotrop.label' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - need example ; ; End of Example 1 ;
_item_description.description ; These are the standard anisotropic atomic displacement components which appear in the structure factor term: exp(-1/4 sum~i~ sum~j~ B~ij~ h~i~ h~j~ a*~i~ a*~j~). The unique components of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.B' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U' 'constant' '_atom_site_anisotrop.U' 'constant' '_atom_site.aniso_B' 'alternative_exclusive' '_atom_site.aniso_U' 'alternative_exclusive' '_atom_site_anisotrop.U' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
save_atom_site_anisotrop.B_esd.
_item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B. ; _item.name '_atom_site_anisotrop.B_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U_esd' 'constant' '_atom_site_anisotrop.U_esd' 'constant' '_atom_site.aniso_B_esd' 'alternative_exclusive' '_atom_site.aniso_U_esd' 'alternative_exclusive' '_atom_site_anisotrop.U_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site_anisotrop.label.
_item_description.description ; This data item is a pointer to _atom_site.label in the ATOM_SITE category. ;
save_atom_site_anisotrop.ratio.
_item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site_anisotrop.ratio' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 1.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_ratio' 'alternative_exclusive' _item_type.code float
_item_description.description ; These are the standard anisotropic atomic displacement components which appear in the structure factor term: exp(-2pi^2^ sum~i~ sum~j~ U~ij~ h~i~ h~j~ a*~i~ a*~j~). The unique components of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B' 'constant' '_atom_site_anisotrop.B' 'constant' '_atom_site.aniso_B' 'alternative_exclusive' '_atom_site.aniso_U' 'alternative_exclusive' '_atom_site_anisotrop.B' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_squared'
save_atom_site_anisotrop.U_esd.
_item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U. ; _item.name '_atom_site_anisotrop.U_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B_esd' 'constant' '_atom_site_anisotrop.B_esd' 'constant' '_atom_site.aniso_B_esd' 'alternative_exclusive' '_atom_site.aniso_U_esd' 'alternative_exclusive' '_atom_site_anisotrop.B_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
_category.description ; Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. ; _category.id _category.id _category.mandatory_code no _category_key.name '_atom_sites.block_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and/or laboratory records for the structure corresponding to PDB entry 5HVP (Using simple matrix input) ; ; _atom_sites.cartn_transform_axes 'c along z, astar along x, b along y' _atom_sites.cartn_tran_matrix 58.39 0.00 0.00 0.00 86.70 0.00 0.00 0.00 46.27 ; ; Example 2 - based on PDB entry 5HVP and/or laboratory records for the structure corresponding to PDB entry 5HVP (Using matrix element enumeration) ; ; _atom_sites.cartn_transform_axes 'c along z, astar along x, b along y' _atom_sites.cartn_tran_matrix[1][1] 58.39 _atom_sites.cartn_tran_matrix[1][2] 0.00 _atom_sites.cartn_tran_matrix[1][3] 0.00 _atom_sites.cartn_tran_matrix[2][1] 0.00 _atom_sites.cartn_tran_matrix[2][2] 86.70 _atom_sites.cartn_tran_matrix[2][3] 0.00 _atom_sites.cartn_tran_matrix[3][1] 0.00 _atom_sites.cartn_tran_matrix[3][2] 0.00 _atom_sites.cartn_tran_matrix[3][3] 46.27 ;
save_atom_sites.cartn_tran_matrix.
_item_description.description ; The matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.cartn_transform_axes. |11 12 13| x x' |21 22 23| ( y ) fractional = ( y' ) Cartesian |31 32 33| z z' ; _item.name '_atom_sites.cartn_tran_matrix' _item.category_id _item.category_id _item.mandatory_code no _item_structure.code 'matrix3x3' _item_structure.organization 'rowwise' _item_type.code float
save_atom_sites.cartn_tran_matrix[1][1].
_item_description.description ; The [1][1] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[1][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_11' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[1][2].
_item_description.description ; The [1][2] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[1][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_12' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[1][3].
_item_description.description ; The [1][3] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[1][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_13' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[2][1].
_item_description.description ; The [2][1] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[2][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_21' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[2][2].
_item_description.description ; The [2][2] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[2][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_22' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[2][3].
_item_description.description ; The [2][3] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[2][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_21' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[3][1].
_item_description.description ; The [3][1] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[3][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_31' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[3][2].
_item_description.description ; The [3][2] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[3][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_32' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_tran_matrix[3][3].
_item_description.description ; The [3][3] element of the 3x3 matrix atom_sites.cartn_tran_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_atom_sites.cartn_tran_matrix[3][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_tran_matrix_33' _item_related.related_name '_atom_sites.cartn_tran_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_atom_sites.cartn_transform_axes.
_item_description.description ; A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transform- ation matrix _atom_sites.cartn_tran_matrix ; _item.name '_atom_sites.cartn_transform_axes' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_sites_cartn_transform_axes' _item_type.code char _item_examples.case 'a parallel to x; b in the plane of y & z'
save_atom_sites.frac_tran_matrix.
_item_description.description ; The matrix used to transform Cartesian coordinates in the ATOM_SITE category fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.cartn_transform_axes. |11 12 13| x x' |21 22 23| ( y ) Cartesian = ( y' ) fractional |31 32 33| z z' ; _item.name '_atom_sites.frac_tran_matrix' _item.category_id _item.category_id _item.mandatory_code no _item_structure.code 'matrix3x3' _item_structure.organization 'rowwise' _item_type.code float
save_atom_sites.solution_hydrogens.
_item_description.description ; A codes which identifies the methods used to locate the initial atomic sites. The solution_hydrogens code identifies how the hydrogens were located. ; _item.name '_atom_sites.solution_hydrogens' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods'
save_atom_sites.solution_primary.
_item_description.description ; A code which identifies the methods used to locate the initial atomic sites. The solution_primary code identifies how the first atom sites were determined. ; _item.name '_atom_sites.solution_primary' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods'
save_atom_sites.solution_secondary.
_item_description.description ; A code which identifies the methods used to locate the initial atomic sites. The solution_secondary code identifies how the non-hydrogen sites not include in solution_primary were located. ; _item.name '_atom_sites.solution_secondary' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods'
_category.description ; Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this CIF. ; _category.id _category.id _category.mandatory_code no _category_key.name '_atom_sites_alt.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_alt.id _atom_sites_alt.details '.' ; Atom sites with the alternative id set to null are not modelled in alternative conformations ; '1' ; Atom sites with the alternative id set to 1 have been modelled in alternative conformations with respect to atom sites marked with alternative id 2. The conformations of amino acid side chains and solvent atoms with alternative id set to 1 correlate with the conformation of the inhibitor marked with alternative id 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor. ; '2' ; Atom sites with the alternative id set to 2 have been modelled in alternative conformations with respect to atom sites marked with alternative id 1. The conformations of amino acid side chains and solvent atoms with alternative id set to 2 correlate with the conformation of the inhibitor marked with alternative id 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor. ; '3' ; Atom sites with the alternative id set to 3 have been modelled in alternative conformations with respect to atoms marked with alternative id 4. The conformations of amino acid side chains and solvent atoms with alternative id set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; '4' ; Atom sites with the alternative id set to 4 have been modelled in alternative conformations with respect to atoms marked with alternative id 3. The conformations of amino acid side chains and solvent atoms with alternative id set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; ;
_item_description.description ; A description of special aspects of the modeling of atoms in alternative conformations. ; _item.name '_atom_sites_alt.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code text
_item_description.description ; The value of _atom_sites_alt.id must uniquely identify a record in the _atom_sites_alt. list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt.id' atom_sites_alt yes '_atom_site.label_alt_id' atom_site yes '_atom_sites_alt_gen.alt_id' atom_sites_alt_gen yes '_struct_conn.ptnr1_label_alt_id' struct_conn yes '_struct_conn.ptnr2_label_alt_id' struct_conn yes '_struct_mon_nucl.label_alt_id' struct_mon_nucl yes '_struct_mon_prot.label_alt_id' struct_mon_prot yes '_struct_mon_prot_cis.label_alt_id' struct_mon_prot_cis yes '_struct_ncs_dom_gen.beg_label_alt_id' struct_ncs_dom_gen yes '_struct_ncs_dom_gen.end_label_alt_id' struct_ncs_dom_gen yes '_struct_site_gen.label_alt_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_alt_id' '_atom_sites_alt.id' '_atom_sites_alt_gen.alt_id' '_atom_sites_alt.id' '_struct_conn.ptnr1_label_alt_id' '_atom_site.label_alt_id' '_struct_conn.ptnr2_label_alt_id' '_atom_site.label_alt_id' '_struct_mon_nucl.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot_cis.label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_gen.beg_label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_gen.end_label_alt_id' '_atom_site.label_alt_id' '_struct_site_gen.label_alt_id' '_atom_site.label_alt_id' _item_type.code char loop_ _item_examples.case 'Orientation 1' 'Molecule abc'
_item_description.description ; The value of _atom_sites_alt.id must uniquely identify a record in the _atom_sites_alt. list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt.id' atom_sites_alt yes '_atom_site.label_alt_id' atom_site yes '_atom_sites_alt_gen.alt_id' atom_sites_alt_gen yes '_struct_conn.ptnr1_label_alt_id' struct_conn yes '_struct_conn.ptnr2_label_alt_id' struct_conn yes '_struct_mon_nucl.label_alt_id' struct_mon_nucl yes '_struct_mon_prot.label_alt_id' struct_mon_prot yes '_struct_mon_prot_cis.label_alt_id' struct_mon_prot_cis yes '_struct_ncs_dom_gen.beg_label_alt_id' struct_ncs_dom_gen yes '_struct_ncs_dom_gen.end_label_alt_id' struct_ncs_dom_gen yes '_struct_site_gen.label_alt_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_alt_id' '_atom_sites_alt.id' '_atom_sites_alt_gen.alt_id' '_atom_sites_alt.id' '_struct_conn.ptnr1_label_alt_id' '_atom_site.label_alt_id' '_struct_conn.ptnr2_label_alt_id' '_atom_site.label_alt_id' '_struct_mon_nucl.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot_cis.label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_gen.beg_label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_gen.end_label_alt_id' '_atom_site.label_alt_id' '_struct_site_gen.label_alt_id' '_atom_site.label_alt_id' _item_type.code char loop_ _item_examples.case 'Orientation 1' 'Molecule abc'
_category.description ; Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation ids. ; _category.id _category.id _category.mandatory_code no _category_key.name '_atom_sites_alt_ens.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_alt_ens.id _atom_sites_alt_ens.details 'Ensemble 1-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric, alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (id=1) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 1-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (id=1) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (id=2) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (id=2) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; ;
save_atom_sites_alt_ens.details.
_item_description.description ; A description of special aspects of the ensemble structure generated from atoms with various alternative ids. ; _item.name '_atom_sites_alt_ens.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code text
_item_description.description ; The value of _atom_sites_alt_ens.id must uniquely identify a record in the _atom_sites_alt_ens. list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt_ens.id' atom_sites_alt_ens yes '_atom_sites_alt_gen.ens_id' atom_sites_alt_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_ens.id' _item_type.code char
_category.description ; Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_gen.alt_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_alt_gen.ens_id _atom_sites_alt_gen.alt_id 'Ensemble 1-A' '.' 'Ensemble 1-A' '1' 'Ensemble 1-A' '3' 'Ensemble 1-B' '.' 'Ensemble 1-B' '1' 'Ensemble 1-B' '4' 'Ensemble 2-A' '.' 'Ensemble 2-A' '2' 'Ensemble 2-A' '3' 'Ensemble 2-B' '.' 'Ensemble 2-B' '2' 'Ensemble 2-B' '4' ;
save_atom_sites_alt_gen.alt_id.
_item_description.description ; This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_atom_sites_alt_gen.ens_id.
_item_description.description ; This data item is a pointer to _atom_sites_alt_ens.id in the ATOM_SITES_ALT_ENS category. ;
_category.description ; Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or group of atom sites. ; _category.id _category.id _category.mandatory_code no _category_key.name '_atom_sites_footnote.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_footnote.id _atom_sites_footnote.text 1 ; The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative ids *1* and *2*. ; 2 ; Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative id *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative id *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 3 ; The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative id *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative id *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 4 ; Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor. ; 5 ; The positions of these water molecules correlate with alternative orientations of amino acid side chains that do not correlate with alternative orientations of the inhibitor. ; ;
_item_description.description ; A code that identifies the footnote. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_footnote.id' atom_sites_footnote yes '_atom_site.footnote_id' atom_site no loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.footnote_id' '_atom_sites_footnote.id' _item_type.code code loop_ _item_examples.case a b 1 2
_item_description.description ; A code that identifies the footnote. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_footnote.id' atom_sites_footnote yes '_atom_site.footnote_id' atom_site no loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.footnote_id' '_atom_sites_footnote.id' _item_type.code code loop_ _item_examples.case a b 1 2
save_atom_sites_footnote.text.
_item_description.description ; The text of the footnote. Footnotes are used to describe an atom site or group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modelled, among many other possibilities. ; _item.name '_atom_sites_footnote.text' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the ATOM_TYPE category record details about properties of the atoms that occupy the atom sites, such as the atomic scattering factors. ; _category.id _category.id _category.mandatory_code no _category_key.name '_atom_type.symbol' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c C 0 2.31000 20.8439 1.02000 10.2075 1.58860 0.568700 0.865000 51.6512 0.21560 N 0 12.2126 0.005700 3.13220 9.89330 2.01250 28.9975 1.16630 0.582600 -11.529 O 0 3.04850 13.2771 2.28680 5.70110 1.54630 0.323900 0.867000 32.9089 0.250800 S 0 6.90530 1.46790 5.20340 22.2151 1.43790 0.253600 1.58630 56.1720 0.866900 CL -1 18.2915 0.006600 7.20840 1.17170 6.53370 19.5424 2.33860 60.4486 -16.378 ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.number_in_cell _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_source C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B ;
save_atom_type.analytical_mass_%.
_item_description.description ; Mass percentage of this atom type derived from chemical analysis. ; _item.name '_atom_type.analytical_mass_%' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_analytical_mass_%' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description ; A description of the atom(s) designated by this atom type. In most cases this will be the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. ; _item.name '_atom_type.description' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_description' _item_type.code char loop_ _item_examples.case deuterium 0.34Fe+0.66Ni
save_atom_type.number_in_cell.
_item_description.description ; Total number of atoms of this atom type in the unit cell. ; _item.name '_atom_type.number_in_cell' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_number_in_cell' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_atom_type.oxidation_number.
_item_description.description ; Formal oxidation state of this atom type in the structure. ; _item.name '_atom_type.oxidation_number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_oxidation_number' _item_default.value 0 _item_range.maximum 6 _item_range.minimum -6 _item_type.code int
_item_description.description ; The effective intrarmolecular bonding radii of this atom type. ; _item.name '_atom_type.radius_bond' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_bond' _item_range.maximum 4.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_atom_type.radius_contact.
_item_description.description ; The effective intermolecular bonding radii of this atom type. ; _item.name '_atom_type.radius_contact' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_contact' _item_range.maximum 4.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_atom_type.scat_Cromer_Mann_a1.
_item_description.description ; The a1 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_a1' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a1' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_a2.
_item_description.description ; The a2 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_a2' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a2' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_a3.
_item_description.description ; The a3 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_a3' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a3' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_a4.
_item_description.description ; The a4 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_a4' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a4' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_b1.
_item_description.description ; The b1 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_b1' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b1' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_b2.
_item_description.description ; The b2 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_b2' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b2' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_b3.
_item_description.description ; The b3 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_b3' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b3' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_b4.
_item_description.description ; The b4 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_b4' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b4' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_c' _item_type.code float
save_atom_type.scat_Cromer_Mann_c.
_item_description.description ; The c Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. See International Tables for X-ray Crystallography, Vol. IV, Table 2.2B (1974); or International Tables for Crystallography, Vol. C, Tables 6.1.1.4 and 6.1.1.5 (1991). ; _item.name '_atom_type.scat_Cromer_Mann_c' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_c' loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' _item_type.code float
save_atom_type.scat_dispersion_imag.
_item_description.description ; The imaginary component of the anomalous dispersion scattering factors, f'' and f' (in electrons) for this atom type and the radiation given in _diffrn_radiation.wavelength. ; _item.name '_atom_type.scat_dispersion_imag' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_imag' _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_real' _item_type.code float
save_atom_type.scat_dispersion_real.
_item_description.description ; The real component of the anomalous dispersion scattering factors, f'' and f' (in electrons) for this atom type and the radiation given in _diffrn_radiation.wavelength. ; _item.name '_atom_type.scat_dispersion_real' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_real' _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_imag' _item_type.code float
_item_description.description ; Reference to source of scattering factors used for this atom type ; _item.name '_atom_type.scat_source' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_source' _item_type.code float _item_examples.case 'International Tables Vol IV Table 2.4.6B'
save_atom_type.scat_versus_stol_list.
_item_description.description ; A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended ; _item.name '_atom_type.scat_versus_stol_list' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_versus_stol_list' _item_type.code char
_item_description.description ; The code used to identify the atom specie(s) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underline with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_type.symbol' atom_type yes '_atom_site.type_symbol' atom_site yes '_atom_site_anisotrop.type_symbol' atom_site_anisotrop yes '_chemical_conn_atom.type_symbol' chemical_conn_atom yes '_entity_mon_atom.type_symbol' entity_mon_atom yes '_phasing_MIR_site.atom_type_symbol' phasing_MIR_der yes _item_aliases.alias_name '_atom_type_symbol' loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.type_symbol' '_atom_type.symbol' '_atom_site_anisotrop.type_symbol' '_atom_type.symbol' '_chemical_conn_atom.type_symbol' '_atom_type.symbol' '_entity_mon_atom.type_symbol' '_atom_type.symbol' '_phasing_MIR_site.atom_type_symbol' '_atom_type.symbol' _item_type.code code loop_ _item_examples.case C Cu2+ H(SDS) dummy FeNi
_item_description.description ; The code used to identify the atom specie(s) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underline with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_type.symbol' atom_type yes '_atom_site.type_symbol' atom_site yes '_atom_site_anisotrop.type_symbol' atom_site_anisotrop yes '_chemical_conn_atom.type_symbol' chemical_conn_atom yes '_entity_mon_atom.type_symbol' entity_mon_atom yes '_phasing_MIR_site.atom_type_symbol' phasing_MIR_der yes _item_aliases.alias_name '_atom_type_symbol' loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.type_symbol' '_atom_type.symbol' '_atom_site_anisotrop.type_symbol' '_atom_type.symbol' '_chemical_conn_atom.type_symbol' '_atom_type.symbol' '_entity_mon_atom.type_symbol' '_atom_type.symbol' '_phasing_MIR_site.atom_type_symbol' '_atom_type.symbol' _item_type.code code loop_ _item_examples.case C Cu2+ H(SDS) dummy FeNi
_item_description.description ; The code used to identify the atom specie(s) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underline with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_type.symbol' atom_type yes '_atom_site.type_symbol' atom_site yes '_atom_site_anisotrop.type_symbol' atom_site_anisotrop yes '_chemical_conn_atom.type_symbol' chemical_conn_atom yes '_entity_mon_atom.type_symbol' entity_mon_atom yes '_phasing_MIR_site.atom_type_symbol' phasing_MIR_der yes _item_aliases.alias_name '_atom_type_symbol' loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.type_symbol' '_atom_type.symbol' '_atom_site_anisotrop.type_symbol' '_atom_type.symbol' '_chemical_conn_atom.type_symbol' '_atom_type.symbol' '_entity_mon_atom.type_symbol' '_atom_type.symbol' '_phasing_MIR_site.atom_type_symbol' '_atom_type.symbol' _item_type.code code loop_ _item_examples.case C Cu2+ H(SDS) dummy FeNi
_category.description ; Data items in the AUDIT category record details about the creation and subsequent updating of the CIF. ; _category.id _category.id _category.mandatory_code no _category_key.name '_audit.revision_id' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _audit.creation_date '1992-12-08' _audit.creation_method ; Created by hand from PDB entry 5HVP, from the JBC paper describing this structure and from laboratory records ; _audit.update_record ; 1992-12-09 adjusted to reflect comments from Brian McKeever 1992-12-10 adjusted to reflect comments from Helen Berman 1992-12-12 adjusted to reflect comments from Keith Watenpaugh ; ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _audit.creation_date 1991-03-20 _audit.creation_method from_xtal_archive_file_using_CIFIO _audit.update_record ; 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec'd by co-editor with diagram as manuscript HL7. 1991-04-17 adjustments based on first referees report. 1991-04-18 adjustments based on second referees report. ; ;
_item_description.description ; A date that the CIF was created. The date format is yyyy-mm-dd. ; _item.name '_audit.creation_date' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_audit_creation_date' _item_type.code char _item_examples.case 1990-07-12
_item_description.description ; A description of how data was entered into the CIF. ; _item.name '_audit.creation_method' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_audit_creation_method' _item_type.code char _item_examples.case 'spawned by the program QBEE'
_item_description.description ; The value of _audit.revision_id must uniquely identify a record in the AUDIT list. ; _item.name '_audit.revision_id' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'rev1'
_item_description.description ; A record of any changes to the CIF. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. ; _item.name '_audit.update_record' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_audit_update_record' _item_type.code char _item_examples.case '1990-07-15 Updated by the Co-editor'
_category.description ; Data items in the AUDIT_AUTHOR category record details about the author(s) of the CIF. ; _category.id _category.id _category.mandatory_code no _category_key.name '_audit_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _audit_author.name _audit_author.address 'Fitzgerald, Paula M.D.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'McKeever, Brian M.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Van Middlesworth, J.F.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Springer, James P.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; ;
_item_description.description ; The address of an author of this CIF. If there are multiple authors, _audit_author.address will be looped with _audit_author.name. ; _item.name '_audit_author.address' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Department Institute Street City and postcode COUNTRY ;
_item_description.description ; The name of an author of this CIF. If there are multiple authors, _audit_author.name will be looped with _audit_author.address. The family name(s) followed by a comma, precedes the first name(s) or initial(s). ; _item.name '_audit_author.name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A'
_category.description ; Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this CIF. ; _category.id _category.id _category.mandatory_code no _category_key.name '_audit_contact_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _audit_contact_author.name 'Fitzgerald, Paula M.D.' _audit_contact_author.address ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; _audit_contact_author.phone '908 594 5510' _audit_contact_author.fax '908 594 6645' _audit_contact_author.email 'paula_fitzgerald@merck.com' ;
save_audit_contact_author.address.
_item_description.description ; The mailing address of the author of the CIF to whom correspon- dence should be addressed. ; _item.name '_audit_contact_author.address' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Department Institute Street City and postcode COUNTRY ;
save_audit_contact_author.email.
_item_description.description ; The electronic mail address of the author of the CIF to whom correspondence should be addressed, in a form recognisable to international networks. ; _item.name '_audit_contact_author.email' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case name@host.domain.country uur5@banjo.bitnet
save_audit_contact_author.fax.
_item_description.description ; The facsimile telephone number of the author of the CIF to whom correspondence should be addressed. The international code is given in brackets and any extension number is preceded by 'ext'. ; _item.name '_audit_contact_author.fax' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case '(12) 34 947 7334'
save_audit_contact_author.name.
_item_description.description ; The name of the author of the CIF to whom correspondence should be addressed. The family name(s) followed by a comma, precedes the first name(s) or initial(s). ; _item.name '_audit_contact_author.name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A'
save_audit_contact_author.phone.
_item_description.description ; The telephone number of the author of the CIF to whom correspondence should be addressed. The international code is given in brackets and any extension number is preceded by 'ext'. ; _item.name '_audit_contact_author.phone' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case '(12) 34 947 7330 ext 5543'
_category.description ; There is only one item in the BLOCK category, _block.id. This data item gives a name to the data block, an indirectly a key to the categories (such as CELL, GEOM, EXPTL) that desribe information pertinent to the entire data block. ; _category.id _category.id _category.mandatory_code no _category_key.name '_block.id' loop_ _category_group.id 'inclusive_group' 'block_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _block.id 5HVP ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _block.id TOZ ;
_item_description.description ; The value of _block.id identies the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_block.id' block yes '_atom_sites.block_id' atom_sites yes '_cell.block_id' cell yes '_cell_measurement.block_id' cell_measurement yes '_chemical.block_id' chemical yes '_chemical_formula.block_id' chemical_formula yes '_computing.block_id' computing yes '_database.block_id' database yes '_diffrn.block_id' diffrn yes '_diffrn_measurement.block_id' diffrn_measurement yes '_diffrn_orient_matrix.block_id' diffrn_orient_matrix yes '_diffrn_radiation.block_id' diffrn_radiation yes '_diffrn_reflns.block_id' diffrn_reflns yes '_diffrn_standards.block_id' diffrn_standards yes '_exptl.block_id' exptl yes '_geom.block_id' geom yes '_journal.block_id' journal yes '_phasing_averaging.block_id' phasing_averaging yes '_phasing_isomorphous.block_id' phasing_isomorphous yes '_phasing_MAD.block_id' phasing_MAD yes '_phasing_MIR.block_id' phasing_MIR yes '_phasing_MR.block_id' phasing_MR yes '_publ.block_id' publ yes '_publ_manuscript_incl.block_id' publ_manuscript_incl yes '_refine.block_id' refine yes '_reflns.block_id' reflns yes '_struct.block_id' struct yes '_struct_mon_details.block_id' struct_mon_details yes '_symmetry.block_id' symmetry yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites.block_id' '_block.id' '_cell.block_id' '_block.id' '_cell_measurement.block_id' '_block.id' '_chemical.block_id' '_block.id' '_chemical_formula.block_id' '_block.id' '_computing.block_id' '_block.id' '_database.block_id' '_block.id' '_diffrn.block_id' '_block.id' '_diffrn_measurement.block_id' '_block.id' '_diffrn_orient_matrix.block_id' '_block.id' '_diffrn_radiation.block_id' '_block.id' '_diffrn_reflns.block_id' '_block.id' '_diffrn_standards.block_id' '_block.id' '_exptl.block_id' '_block.id' '_geom.block_id' '_block.id' '_journal.block_id' '_block.id' '_phasing_averaging.block_id' '_block.id' '_phasing_isomorphous.block_id' '_block.id' '_phasing_MAD.block_id' '_block.id' '_phasing_MIR.block_id' '_block.id' '_phasing_MR.block_id' '_block.id' '_publ.block_id' '_block.id' '_publ_manuscript_incl.block_id' '_block.id' '_refine.block_id' '_block.id' '_reflns.block_id' '_block.id' '_struct.block_id' '_block.id' '_struct_mon_details.block_id' '_block.id' '_symmetry.block_id' '_block.id' _item_type.code char
_item_description.description ; The value of _block.id identies the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_block.id' block yes '_atom_sites.block_id' atom_sites yes '_cell.block_id' cell yes '_cell_measurement.block_id' cell_measurement yes '_chemical.block_id' chemical yes '_chemical_formula.block_id' chemical_formula yes '_computing.block_id' computing yes '_database.block_id' database yes '_diffrn.block_id' diffrn yes '_diffrn_measurement.block_id' diffrn_measurement yes '_diffrn_orient_matrix.block_id' diffrn_orient_matrix yes '_diffrn_radiation.block_id' diffrn_radiation yes '_diffrn_reflns.block_id' diffrn_reflns yes '_diffrn_standards.block_id' diffrn_standards yes '_exptl.block_id' exptl yes '_geom.block_id' geom yes '_journal.block_id' journal yes '_phasing_averaging.block_id' phasing_averaging yes '_phasing_isomorphous.block_id' phasing_isomorphous yes '_phasing_MAD.block_id' phasing_MAD yes '_phasing_MIR.block_id' phasing_MIR yes '_phasing_MR.block_id' phasing_MR yes '_publ.block_id' publ yes '_publ_manuscript_incl.block_id' publ_manuscript_incl yes '_refine.block_id' refine yes '_reflns.block_id' reflns yes '_struct.block_id' struct yes '_struct_mon_details.block_id' struct_mon_details yes '_symmetry.block_id' symmetry yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites.block_id' '_block.id' '_cell.block_id' '_block.id' '_cell_measurement.block_id' '_block.id' '_chemical.block_id' '_block.id' '_chemical_formula.block_id' '_block.id' '_computing.block_id' '_block.id' '_database.block_id' '_block.id' '_diffrn.block_id' '_block.id' '_diffrn_measurement.block_id' '_block.id' '_diffrn_orient_matrix.block_id' '_block.id' '_diffrn_radiation.block_id' '_block.id' '_diffrn_reflns.block_id' '_block.id' '_diffrn_standards.block_id' '_block.id' '_exptl.block_id' '_block.id' '_geom.block_id' '_block.id' '_journal.block_id' '_block.id' '_phasing_averaging.block_id' '_block.id' '_phasing_isomorphous.block_id' '_block.id' '_phasing_MAD.block_id' '_block.id' '_phasing_MIR.block_id' '_block.id' '_phasing_MR.block_id' '_block.id' '_publ.block_id' '_block.id' '_publ_manuscript_incl.block_id' '_block.id' '_refine.block_id' '_block.id' '_reflns.block_id' '_block.id' '_struct.block_id' '_block.id' '_struct_mon_details.block_id' '_block.id' '_symmetry.block_id' '_block.id' _item_type.code char
_category.description ; Data items in the CELL category record details about the crystallographic cell parameters. ; _category.id _category.id _category.mandatory_code no _category_key.name '_cell.block_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _cell.length_a 58.39(5) _cell.length_b 86.70(12) _cell.length_c 46.27(6) _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.volume 234237 _cell.details ; The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean. ; ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _cell.length_a 5.959(1) _cell.length_b 14.956(1) _cell.length_c 19.737(3) _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.volume 1759.0(3) ;
_item_description.description ; Unit-cell angle alpha in degrees of the reported structure. ; _item.name '_cell.angle_alpha' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle' _item_aliases.alias_name '_cell_angle_alpha' _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_beta' '_cell.angle_gamma' _item_range.maximum 180.0 _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _cell.angle_alpha. ; _item.name '_cell.angle_alpha_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_beta_esd' '_cell.angle_gamma_esd' _item_type.code float _item_units.code 'degrees'
_item_description.description ; Unit-cell angle beta in degrees of the reported structure. ; _item.name '_cell.angle_beta' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle' _item_aliases.alias_name '_cell_angle_beta' _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_gamma' _item_range.maximum 180.0 _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _cell.angle_beta. ; _item.name '_cell.angle_beta_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_gamma_esd' _item_type.code float _item_units.code 'degrees'
_item_description.description ; Unit-cell angle gamma in degrees of the reported structure. ; _item.name '_cell.angle_gamma' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle' _item_aliases.alias_name '_cell_angle_gamma' _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_beta' _item_range.maximum 180.0 _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _cell.angle_gamma. ; _item.name '_cell.angle_gamma_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_beta_esd' _item_type.code float _item_units.code 'degrees'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; A description of special aspects of the cell choice, noting possible alternative settings. ; _item.name '_cell.details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_special_details' _item_type.code char loop_ _item_examples.case 'pseudo-orthorhombic' ; standard setting from 45 deg rotation around c ;
_item_description.description ; The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum. ; _item.name '_cell.formula_units_Z' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_formula_units_Z' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
_item_description.description ; Unit-cell length a corresponding to the structure reported. ; _item.name '_cell.length_a' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length' _item_aliases.alias_name '_cell_length_a' loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _cell.length_a. ; _item.name '_cell.length_a_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_b_esd' '_cell.length_c_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Unit-cell length b corresponding to the structure reported. ; _item.name '_cell.length_b' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length' _item_aliases.alias_name '_cell_length_b' loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _cell.length_b. ; _item.name '_cell.length_b_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_c_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Unit-cell length c corresponding to the structure reported. ; _item.name '_cell.length_c' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length' _item_aliases.alias_name '_cell_length_c' loop_ _item_dependent.dependent_name '_cell.length_a' '_cell.length_b' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _cell.length_c. ; _item.name '_cell.length_c_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_b_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Volume calculated from the values of _cell.length_a, _cell.length_b, _cell.length_c, _cell.angle_alpha, _cell.angle_beta, and _cell.angle_gamma. %% Need real formula here. ; _item.name '_cell.volume' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_volume' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_cubed'
_item_description.description ; The estimated standard deviation of _cell.volume. ; _item.name '_cell.volume_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms_cubed'
_category.description ; Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. ; _category.id _category.id _category.mandatory_code no _category_key.name '_cell_measurement.block_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _cell_measurement.temperature 293(3) _cell_measurement.theta_min 11 _cell_measurement.theta_max 31 _cell_measurement.wavelength 1.54 ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _cell_measurement.temperature 293 _cell_measurement.reflns_used 25 _cell_measurement.theta_min 25 _cell_measurement.theta_max 31 ;
save_cell_measurement.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_cell_measurement.pressure.
_item_description.description ; The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure used to synthesize the sample). ; _item.name '_cell_measurement.pressure' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_pressure' _item_type.code float _item_type_conditions.code esd _item_units.code 'kilopascals'
save_cell_measurement.pressure_esd.
_item_description.description ; The estimated standard deviation of _cell_measurement.pressure. ; _item.name '_cell_measurement.pressure_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kilopascals'
save_cell_measurement.radiation.
_item_description.description ; Description of the radiation used to measure the unit-cell data. See also _cell_measurement.wavelength. ; _item.name '_cell_measurement.radiation' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_radiation' _item_type.code char loop_ _item_examples.case 'neutron' 'Cu K\a' 'synchrotron'
save_cell_measurement.reflns_used.
_item_description.description ; The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. ; _item.name '_cell_measurement.reflns_used' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_reflns_used' _item_type.code int
save_cell_measurement.temperature.
_item_description.description ; The temperature in degrees Kelvin at which the unit-cell parameters were measured (not the temperature of synthesis). ; _item.name '_cell_measurement.temperature' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_temperature' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'kelvin'
save_cell_measurement.temperature_esd.
_item_description.description ; The estimated standard deviation of _cell_measurement.temperature. ; _item.name '_cell_measurement.temperature_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kelvin'
save_cell_measurement.theta_max.
_item_description.description ; The maximum theta angle in degrees of reflections used to measure the unit cell. ; _item.name '_cell_measurement.theta_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_max' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_cell_measurement.theta_min.
_item_description.description ; The minimum theta angle in degrees of reflections used to measure the unit cell. ; _item.name '_cell_measurement.theta_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_min' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_cell_measurement.wavelength.
_item_description.description ; The wavelength of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be the same as that given in _diffrn_radiation.wavelength. ; _item.name '_cell_measurement.wavelength' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_wavelength' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_category.description ; Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used in determination of the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ;
save_cell_measurement_refln.index_h.
_item_description.description ; Miller index h of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_cell_measurement_refln_index_h' loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' _item_type.code int
save_cell_measurement_refln.index_k.
_item_description.description ; Miller index k of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_cell_measurement_refln_index_k' loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_l' _item_type.code int
save_cell_measurement_refln.index_l.
_item_description.description ; Miller index l of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_cell_measurement_refln_index_l' loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' _item_type.code int
save_cell_measurement_refln.theta.
_item_description.description ; Theta angle in degrees of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.theta' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_refln_theta' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
_category.description ; Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. Data items in the CHEMICAL category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. ; _category.id _category.id _category.mandatory_code no _category_key.name '_chemical.block_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; _chemical.name_systematic trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-1,3-oxazolidin-5-one ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_chemical.compound_source.
_item_description.description ; Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. ; _item.name '_chemical.compound_source' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_compound_source' _item_type.code char loop_ _item_examples.case 'From Norilsk (USSR)' 'Extracted from the bark of Cinchona Naturalis'
_item_description.description ; The melting point in degees Kelvin of the crystal. ; _item.name '_chemical.melting_point' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_melting_point' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'kelvin'
_item_description.description ; Trivial name by which compound is commonly known. ; _item.name '_chemical.name_common' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_name_common' _item_type.code char _item_examples.case '1-bromoestradiol'
_item_description.description ; Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also _chemical.compound_source. ; _item.name '_chemical.name_mineral' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_name_mineral' _item_type.code char _item_examples.case chalcopyrite
save_chemical.name_structure_type.
_item_description.description ; Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. ; _item.name '_chemical.name_structure_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_name_structure_type' _item_type.code char loop_ _item_examples.case perovskite sphalerite A15
save_chemical.name_systematic.
_item_description.description ; IUPAC or Chemical Abstracts full name of compound. ; _item.name '_chemical.name_systematic' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_name_systematic' _item_type.code char _item_examples.case '1-bromoestra-1,3,5(10)-triene-3,17\b-diol'
_category.description ; Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the 2D chemical structure of the molecular species. They allowa 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. ; _category.id _category.id _category.mandatory_code no _category_key.name '_chemical_conn_atom.number' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 2 ;
save_chemical_conn_atom.charge.
_item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chemical_conn_atom.charge' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_charge' _item_default.value 0 _item_range.maximum 6 _item_range.minimum -6 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion'
save_chemical_conn_atom.display_x.
_item_description.description ; The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. If absent, values will be assigned by the journals' or database staff. ; _item.name '_chemical_conn_atom.display_x' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_x' _item_dependent.dependent_name '_chemical_conn_atom.display_y' _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
save_chemical_conn_atom.display_y.
_item_description.description ; The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. If absent, values will be assigned by the journals' or database staff. ; _item.name '_chemical_conn_atom.display_y' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_y' _item_dependent.dependent_name '_chemical_conn_atom.display_x' _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
_item_description.description ; The Number of Connected Atoms excluding terminal hydrogen atoms. ; _item.name '_chemical_conn_atom.NCA' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NCA' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_item_description.description ; The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number will be the same as _atom_site.attached_hydrogens only if none of the hydrogen atoms appear in the ATOM_SITE list. ; _item.name '_chemical_conn_atom.NH' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NH' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_chemical_conn_atom.number.
_item_description.description ; The chemical sequence number to be associated with this atom. Within an ATOM_SITE list this number must match with one of the _atom_site.chemical_conn_number values. ; loop_ _item.name _item.category_id _item.mandatory_code '_chemical_conn_atom.number' chemical_conn_atom yes '_atom_site.chemical_conn_number' atom_site yes '_chemical_conn_bond.atom_1' chemical_conn_bond yes '_chemical_conn_bond.atom_2' chemical_conn_bond yes _item_aliases.alias_name '_chemical_conn_atom_number' loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.chemical_conn_number' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_1' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_2' '_chemical_conn_atom.number' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
save_chemical_conn_atom.number.
_item_description.description ; The chemical sequence number to be associated with this atom. Within an ATOM_SITE list this number must match with one of the _atom_site.chemical_conn_number values. ; loop_ _item.name _item.category_id _item.mandatory_code '_chemical_conn_atom.number' chemical_conn_atom yes '_atom_site.chemical_conn_number' atom_site yes '_chemical_conn_bond.atom_1' chemical_conn_bond yes '_chemical_conn_bond.atom_2' chemical_conn_bond yes _item_aliases.alias_name '_chemical_conn_atom_number' loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.chemical_conn_number' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_1' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_2' '_chemical_conn_atom.number' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
save_chemical_conn_atom.type_symbol.
_item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item_aliases.alias_name '_chemical_conn_atom_type_symbol'
_category.description ; Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the 2D chemical structure of the molecular species. They allowa 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the _chemical_conn_atom. list and the nature of the chemical bond between these atoms. Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_chemical_conn_bond.atom_1' '_chemical_conn_bond.atom_2' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on ; ; Need Example 2 ;
save_chemical_conn_bond.atom_1.
_item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item_aliases.alias_name '_chemical_conn_bond_atom_1' _item_dependent.dependent_name '_chemical_conn_bond.atom_2'
save_chemical_conn_bond.atom_2.
_item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item_aliases.alias_name '_chemical_conn_bond_atom_2' _item_dependent.dependent_name '_chemical_conn_bond.atom_1'
_item_description.description ; The chemical bond type associated with the connection between the two sites _chemical_conn_bond.atom_1 and *_2. ; _item.name '_chemical_conn_bond.type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_bond_type' _item_default.value sing _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond'
_category.description ; Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and _chemical_formula.sum. For the data item _chemical_formula.moiety the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula.moiety). 1. Only recognized element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count. 4. Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parentheses. That is, all element and group multipliers are assumed to be printed as subscripted numbers. [An exception to this rule exists for _chemical_formula.moiety formulae where pre- and post-multipliers are permitted for molecular units]. 5. Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula.structural, the order of the elements within any group or moiety should be: C, H followed by the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. ; _category.id _category.id _category.mandatory_code no _category_key.name '_chemical_formula.block_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _chemical_formula.moiety 'C18 H25 N O3' _chemical_formula.sum 'C18 H25 N O3' _chemical_formula.weight 303.40 ;
save_chemical_formula.analytical.
_item_description.description ; Formula determined by standard chemical analysis including trace elements. See _chemical_formula.appendix for rules for writing chemical formulae. Parentheses are used only for e.s.d.'s. ; _item.name '_chemical_formula.analytical' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_analytical' _item_type.code char _item_examples.case 'Fe2.45(2) Ni1.60(3) S4'
save_chemical_formula.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; Formula with each discrete bonded residue or ion shown as a separate moiety. See above _chemical_formula.appendix for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: 1. Moieties are separated by commas ','. 2. The order of elements within a moiety follows general rule 5 in _chemical_formula.appendix. 3. Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. 4. Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. ; _item.name '_chemical_formula.moiety' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_moiety' _item_type.code char loop_ _item_examples.case 'C7 H4 Cl Hg N O3 S' 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-' 'C12 H16 N2 O6, 5(H2 O1)' "(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)"
save_chemical_formula.structural.
_item_description.description ; See _chemical_formula.appendix for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom type and atom site data should not be included in this formula (see also _chemical_formula.analytical). ; _item.name '_chemical_formula.structural' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_structural' _item_type.code char loop_ _item_examples.case 'Ca ((Cl O3)2 O)2 (H2 O)6' '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'
_item_description.description ; See _chemical_formula.appendix for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule 5 in _chemical_formula.appendix. Parentheses are not normally used. ; _item.name '_chemical_formula.sum' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_sum' _item_type.code char loop_ _item_examples.case 'C18 H19 N7 O8 S'
_item_description.description ; Formula mass in daltons. This mass should correspond to the formulae given under _chemical_formula.structural, *_moiety or *_sum and, together with the Z value and cell parameters, should yield the density given as _exptl_crystal_density_diffrn. ; _item.name '_chemical_formula.weight' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight' _item_range.maximum ? _item_range.minimum 1.0 _item_type.code float
save_chemical_formula.weight_meas.
_item_description.description ; Formula mass in daltons measured by a non-diffraction experiment. ; _item.name '_chemical_formula.weight_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight_meas' _item_range.maximum ? _item_range.minimum 1.0 _item_type.code float
_category.description ; Data items in the CITATION category record details about the literature cited relevant to the contents of the data block. ; _category.id _category.id _category.mandatory_code no _category_key.name '_citation.id' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _citation.id _citation.coordinate_linkage _citation.title _citation.country _citation.journal_abbrev _citation.journal_volume _citation.journal_issue _citation.page_first _citation.page_last _citation.year _citation.journal_coden_ASTM _citation.journal_coden_ISSN _citation.journal_coden_PDB _citation.book_title _citation.book_publisher _citation.book_coden_ISBN _citation.details primary yes ; Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution. ; US 'J. Biol. Chem.' 265 . 14209 14219 1990 HBCHA3 0021-9258 071 . . . ; The publication that directly relates to this coordinate set. ; 2 no ; Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1. ; UK 'Nature' 337 . 615 619 1989 NATUAS 0028-0836 006 . . . ; Determination of the structure of the unliganded enzyme. ; 3 no ; Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1. ; US 'J. Biol. Chem.' 264 . 1919 1921 1989 HBCHA3 0021-9258 071 . . . ; Crystallization of the unliganded enzyme. ; 4 no ; Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease. ; US 'J. Biol. Chem.' 264 . 2307 2312 1989 HBCHA3 0021-9258 071 . . . ; Expression and purification of the enzyme. ; ;
_item_description.description ; Abstract for the citation. This will be used most when the citation is extracted from a bibliographic database that contains full text or abstract information. ; _item.name '_citation.abstract' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_citation.book_coden_ISBN.
_item_description.description ; The International Standard Book Number (ISBN) code assigned to the book cited; relevant for book chapters. ; _item.name '_citation.book_coden_ISBN' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The name and location of the publisher of the citation; relevant for book chapters. ; _item.name '_citation.book_publisher' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'John Wiley and Sons, New York'
_item_description.description ; The title of the book in which the citation appeared; relevant for book chapters. ; _item.name '_citation.book_title' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_citation.coordinate_linkage.
_item_description.description ; _citation.coordinate_linkage states whether or not this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to creation of the data block, the value of this data item would be no. ; _item.name '_citation.coordinate_linkage' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value yes no
_item_description.description ; The country of publication; relevant for both journal articles and book chapters. ; _item.name '_citation.country' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; A description of special aspects that describe the relationship of the contents of the data block to the literature item cited. ; _item.name '_citation.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; citation relates to this precise coordinate set ; ; citation relates to earlier low-resolution structure ; ; citation relates to further refinement of structure reported in citation 2 ;
_item_description.description ; The value of _citation.id must uniquely identify a record in the CITATION list. The _citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_citation.id' citation yes '_citation_author.citation_id' citation_author yes '_citation_editor.citation_id' citation_editor yes '_comp_prog.citation_id' comp_prog yes loop_ _item_linked.child_name _item_linked.parent_name '_citation_author.citation_id' '_citation.id' '_citation_editor.citation_id' '_citation.id' '_comp_prog.citation_id' '_citation.id' _item_type.code char loop_ _item_examples.case primary 1 2
_item_description.description ; Abbreviated name of the journal cited; abbreviations are according to the rules of ?? ; _item.name '_citation.journal_abbrev' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'J. Mol. Biol.'
save_citation.journal_coden_ASTM.
_item_description.description ; The American Society for Testing of Materials (ASTM) code assigned to the journal cited; relevant for journal articles. ; _item.name '_citation.journal_coden_ASTM' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_citation.journal_coden_ISSN.
_item_description.description ; The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. ; _item.name '_citation.journal_coden_ISSN' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_citation.journal_coden_PDB.
_item_description.description ; The Protein Data Bank (PDB) code assigned to the journal cited; relevant for journal articles. ; _item.name '_citation.journal_coden_PDB' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case '070'
_item_description.description ; Full name of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_full' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'Journal of Molecular Biology'
_item_description.description ; Issue number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_issue' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 2
_item_description.description ; Volume number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_volume' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 174
_item_description.description ; Language in which the citation appears. ; _item.name '_citation.language' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case german
_item_description.description ; Ascession number used by Medline to categorize a specific bibliographic entry. ; _item.name '_citation.Medline_AN' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 1 _item_type.code int _item_examples.case 89064067
_item_description.description ; The first page of the citation; relevant for journal articles and book chapters. ; _item.name '_citation.page_first' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The last page of the citation; relevant for journal articles and book chapters. ; _item.name '_citation.page_last' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The title of the citation; relevant for both journal articles and book chapters. ; _item.name '_citation.title' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Structure of Blah-Blah at 2.1 \%Angstr\"om Resolution. ;
_item_description.description ; The year of the citation; relevant for both journal articles and book chapters. ; _item.name '_citation.year' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int _item_examples.case 1984
_category.description ; Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. ; _category.id _category.id _category.mandatory no loop_ _category_key.name '_citation_author.citation_id' '_citation_author.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and/or laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _citation_author.citation_id _citation_author.name primary 'Fitzgerald, P.M.D.' primary 'McKeever, B.M.' primary 'Van Middlesworth, J.F.' primary 'Springer, J.P.' primary 'Heimbach, J.C.' primary 'Leu, C.-T.' primary 'Herber, W.K.' primary 'Dixon, R.A.F.' primary 'Darke, P.L.' 2 'Navia, M.A.' 2 'Fitzgerald, P.M.D.' 2 'McKeever, B.M.' 2 'Leu, C.-T.' 2 'Heimbach, J.C.' 2 'Herber, W.K.' 2 'Sigal, I.S.' 2 'Darke, P.L.' 2 'Springer, J.P.' 3 'McKeever, B.M.' 3 'Navia, M.A.' 3 'Fitzgerald, P.M.D.' 3 'Springer, J.P.' 3 'Leu, C.-T.' 3 'Heimbach, J.C.' 3 'Herber, W.K.' 3 'Sigal, I.S.' 3 'Darke, P.L.' 4 'Darke, P.L.' 4 'Leu, C.-T.' 4 'Davis, L.J.' 4 'Heimbach, J.C.' 4 'Diehl, R.E.' 4 'Hill, W.S.' 4 'Dixon, R.A.F.' 4 'Sigal, I.S.' ;
save_citation_author.citation_id.
_item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ;
_item_description.description ; Name of an author of the citation; relevant for both journal articles and book chapters. The family name(s) followed by a comma, precedes the first name(s) or initial(s). ; _item.name '_citation_author.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A'
_category.description ; Data items in the CITATION_EDITOR category record details about the editor associated with book chapter citations in the CITATION list. ; _category.id _category.id _category.mandatory no loop_ _category_key.name '_citation_editor.citation_id' '_citation_editor.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - example is completely hypothetical ; ; loop_ _citation_editor.citation_id _citation_editor.name 5 'McKeever, B.M.' 5 'Navia, M.A.' 5 'Fitzgerald, P.M.D.' 5 'Springer, J.P.' ;
save_citation_editor.citation_id.
_item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ;
_item_description.description ; Names of an editor of the citation; relevant for book chapters. The family name(s) followed by a comma, precedes the first name(s) or initial(s). ; _item.name '_citation_editor.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A'
_category.description ; Data items in the COMP_PROG category record details about the computer programs used in the structure analysis. These data items provide an alternative, and more thorough, method for referencing computer programs than do data items in the COMPUTING category. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_comp_prog.task' '_comp_prog.name' '_comp_prog.version' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _comp_prog.task _comp_prog.name _comp.prog.version _comp.prog.citation_id 'data collection' Collect x.x ? 'data reduction' Xengen 1.3 ? 'phasing_MR Merlot 2.2 ? 'molecular graphics' Protein x.x ? 'moleuclar graphics' Frodo x.x ? 'structure refinement' Protin/Prolsq x.x ? ;
_item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ;
_item_description.description ; The task for which the computer program was employed. ; _item.name '_comp_prog.task' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value 'cell refinement' 'data collection' 'data reduction' 'molecular graphics' 'phasing averaging' 'phasing MAD' 'phasing MIR' 'phasing MR' 'publication material' 'structure refinement'
_item_description.description ; The version of the computer program. ; _item.name '_comp_prog.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. ; _category.id _category.id _category.mandatory_code no _category_key.name '_computing.block_id' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _computing.data_collection 'Collect (Siemens)' _computing.data_reduction 'Xengen (Howard)' _computing.phasing_MR 'Merlot (Fitzgerald)' _computing.molecular_graphics 'Protein (Steigemann), Frodo (Jones)' _computing.structure_refinement 'Protin/Prolsq (Konnert, Hendrickson)' ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _computing.data_collection 'Philips PW1100/20 software 1976' _computing.cell_refinement 'LATCON (Xtal: Schwarzenbach & King)' _computing.data_reduction 'pwredu (McLaughlin) ADDREF SORTRF (Xtal)' _computing.structure_solution 'SHELXS86 (Sheldrick)' _computing.structure_refinement 'SHELX76 (Sheldrick) CRYLSQ (Xtal: Olthof)' _computing.publication_material 'BONDLA CIFIO (Xtal: Hall)' ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_computing.cell_refinement.
_item_description.description ; Software used in refining the cell. Give the program or package name and a brief reference. ; _item.name '_computing.cell_refinement' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_computing_cell_refinement' _item_type.code char _item_examples.case 'CAD4 (Enraf Nonius)'
save_computing.data_collection.
_item_description.description ; Software used for data collection. Give the program or package name and a brief reference. ; _item.name '_computing.data_collection' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_computing_data_collection' _item_type.code char _item_examples.case 'CAD4 (Enraf Nonius)'
save_computing.data_reduction.
_item_description.description ; Software used for data reduction. Give the program or package name and a brief reference. ; _item.name '_computing.data_reduction' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_computing_data_reduction' _item_type.code char _item_examples.case 'DIFDAT, SORTRF, ADDREF (XTAL3.0, 1990)'
save_computing.molecular_graphics.
_item_description.description ; Software used for molecular graphics. Give the program or package name and a brief reference. ; _item.name '_computing.molecular_graphics' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_computing_molecular_graphics' _item_type.code char _item_examples.case 'FRODO (Jones, 1986) & ORTEP (Johnson, 1965)'
save_computing.publication_material.
_item_description.description ; Software used for generating material for publication. Give the program or package name and a brief reference. ; _item.name '_computing.publication_material' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_computing_publication_material' _item_type.code char
save_computing.structure_refinement.
_item_description.description ; Software used for refinement of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_refinement' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_computing_structure_refinement' _item_type.code char loop_ _item_examples.case 'SHELX85 (Sheldrick, 1985)' 'X-PLOR (Brunger, 198?)'
save_computing.structure_solution.
_item_description.description ; Software used for solution of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_solution' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_computing_structure_solution' _item_type.code char _item_examples.case 'SHELX85 (Sheldrick, 1985)'
_category.description ; Data items in the DATABASE category have been supercedes by data items in the DATEBASE_NEW category. They are included here only for compliance with older files. ; _category.id _category.id _category.mandatory_code no _category_key.name '_database.block_id' loop_ _category_group.id 'inclusive_group' 'compliance_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _database.code_PDB 5HVP ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The code assigned by Chemical Abstracts. ; _item.name '_database.code_CAS' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_CAS' _item_type.code char
_item_description.description ; The code assigned by Cambridge Structural Data Base (organic and metal-organic compounds). ; _item.name '_database.code_CSD' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_CSD' _item_type.code char
_item_description.description ; The code assigned by the Inorganic Crystal Structure Data Base. ; _item.name '_database.code_ICSD' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_ICSD' _item_type.code char
_item_description.description ; The code assigned by the Metals Data File (metal structures). ; _item.name '_database.code_MDF' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_MDF' _item_type.code char
_item_description.description ; The code assigned by the NBS (NIST) Crystal Data Database (lattice parameters). ; _item.name '_database.code_NBS' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_NBS' _item_type.code char
_item_description.description ; The code assigned by the Powder Diffraction File (JCPDS/ICDD). ; _item.name '_database.code_PDF' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_PDF' _item_type.code char
_item_description.description ; The ASTM coden for a journal as given in the Chemical Source List. ; _item.name '_database.journal_ASTM' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_journal_ASTM' _item_type.code char
_item_description.description ; The journal code used in the Cambridge Structural Database. ; _item.name '_database.journal_CSD' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_journal_CSD' _item_type.code char
_category.description ; Data items in the DATABASE_NEW category record details about the database identifiers of the CIF. These data items are assigned by database managers and should only appear in a CIF if they originate from that source. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_database_new.database_id' '_database_new.database_code' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _database_new.database_id PDB _database_new.database_code 5HVP ;
save_database_new.database_code.
_item_description.description ; The code assigned by the database identified in _database_new.database_id. ; _item.name '_database_new.database_code' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' 'replace' '_database.code_CSD' 'replace' '_database.code_ICSD' 'replace' '_database.code_MDF' 'replace' '_database.code_NBS' 'replace' '_database.code_PDF' 'replace' _item_type.code char loop_ _item_enumeration.value 1ABC ABCDEF
save_database_new.database_id.
_item_description.description ; An abbreviation that identifies the database. ; _item.name '_database_new.database_id' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' 'replace' '_database.code_CSD' 'replace' '_database.code_ICSD' 'replace' '_database.code_MDF' 'replace' '_database.code_NBS' 'replace' '_database.code_PDF' 'replace' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail 'CAS' ; Chemical Abstracts ; 'CSD' ; Cambridge Structural Data Base (organic and metal-organic compounds) ; 'ICSD' ; Inorganic Crystal Structure Data Base ; 'MDF' ; Metals Data File (metal structures) ; 'NDB' ; Nucleic Acids Database ; 'NBS' ; NBS (NIST) Crystal Data Database (lattice parameters) ; 'PDB' ; Protein Data Bank ; 'PDF' ; Powder Diffraction File (JCPDS/ICDD) ;
_category.description ; Data items in the DATABASE_PDB_REMARK category record details about the CIF as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the CIF. These data items are included only for consistency with older PDB format files. They should appear in a CIF only if that CIF was created by reformatting a PDB format file. ; _category.id _category.id _category.mandatory_code no _category_key.name '_database_PDB_remark.num' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _database_PDB_remark.num _database_PDB_remark.text 2 ; RESOLUTION. 2.0 ANGSTROMS. ; 3 ; REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). # - - - - data truncated for brevity - - - - ; ;
_item_description.description ; The value of _database_PDB_remark.num corresponds to the number assigned to the remark in the PDB file. In PDB files, each line of a remark is preceded with REMARK n, where n is the remark number. A given remark may cover any number of lines. In the CIF representation, the remark number is translated into _database_PDB_remark.num and the text of the remark become a single text block, _database_PDB_remark.text. ; _item.name '_database_PDB_remark.num' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code int
save_database_PDB_remark.text.
_item_description.description ; The text of the PDB remark, with the last eight characters (PDB code and PDB record number) excised. Multilined remarks are converted to a single text block (with 'REMARK n ' removed). ; _item.name '_database_PDB_remark.text' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the DATABASE_PDB_REV category record details about the history of the CIF as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a CIF if they originate from that source. ; _category.id _category.id _category.mandatory_code no _category_key.name '_database_PDB_rev.num' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _database_PDB_rev.num _database_PDB_rev.author_name _database_PDB_rev.date _database_PDB_rev.date_original _database_PDB_rev.status _database_PDB_rev.mod_type 1 'Fitzgerald, Paula M.D' 1991-10-15 1990-04-30 'full release' 0 ;
save_database_PDB_rev.author_name.
_item_description.description ; The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma, precedes the first name(s) or initial(s). ; _item.name '_database_PDB_rev.author_name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A'
_item_description.description ; Date the PDB revision took place. Taken from the REVDAT record. ; _item.name '_database_PDB_rev.date' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_database_PDB_rev.date_original.
_item_description.description ; Date the entry first entered the PDB database in the form: yyyy-mm-dd. Taken from the PDB HEADER record. ; _item.name '_database_PDB_rev.date_original' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case '1980-08-21'
save_database_PDB_rev.mod_type.
_item_description.description ; Taken from the REVDAT record. Refer to the Protein Data Bank format description for details. ; _item.name '_database_PDB_rev.mod_type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int loop_ _item_enumeration.value _item_enumeration.detail 0 'initial entry' 1 'all other types of modification' 2 'modifications to CONECT records' 3 ; modifications affecting the coordinates or their transforms (CRYST1, ORIGX, SCALE, MTRIX, TVECT, ATOM, HETATM, SIGATM records) ;
_item_description.description ; The value of _database_PDB_rev.num must uniquely and sequentially identify a record in the _database_PDB_rev. list. Note that this item must be a number, and that modification numbers will be assigned in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_database_PDB_rev.num' database_PDB_rev yes '_database_PDB_rev_record.rev_num' database_PDB_rev_record yes loop_ _item_linked.child_name _item_linked.parent_name '_database_PDB_rev_record.rev_num' '_database_PDB_rev.num' _item_type.code int
save_database_PDB_rev.replaced_by.
_item_description.description ; The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this CIF. ; _item.name '_database_PDB_rev.replaced_by' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_database_PDB_rev.replaces.
_item_description.description ; The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this CIF. ; _item.name '_database_PDB_rev.replaces' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; This definition is preliminary - need to consult with PDB about what they need here. ; _item.name '_database_PDB_rev.status' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value 'in preparation' 'prerelease' 'full release' 'obsolete'
_category.description ; Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a CIF if they originate from that source. ; _category.id _category.id _category.mandatory_code no _category_key.name '_database_PDB_rev_record.rev_num' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - example is completely hypothetical ; ; loop_ _database_PDB_rev_record.rev_num _database_PDB_rev_record.type _database_PDB_rev_record.details 1 CONECT 'Error fix - incorrect connection between atoms 2312 and 2317' 2 MATRIX 'For consistency with 1995-08-04 style-guide' 3 ORIGX 'Based on new data from author' ;
save_database_PDB_rev_record.details.
_item_description.description ; A description of special aspects of the revision of records in this PDB entry. ; _item.name '_database_PDB_rev_record.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Based on new data from author' 'For consistency with 1995-08-04 style-guide' 'For consistency with structural class'
save_database_PDB_rev_record.rev_num.
_item_description.description ; This data item is a pointer to _database_PDB_rev.num in the DATABASE_PDB_REV category. ;
save_database_PDB_rev_record.type.
_item_description.description ; The types of records that were changed in this revision to a PDB entry. ; _item.name '_database_PDB_rev_record.type' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'CRYST1' 'SCALE' 'MTRIX' 'ATOM' 'HETATM'
_category.description ; Data items in the DIFFRN category record details about the diffraction data and its measurement. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn.block_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _diffrn.ambient_temperature 293(3) _diffrn.ambient_environment ; Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air ; _diffrn.crystal_support ; 0.7 mm glass capillary, sealed with dental wax ; _diffrn.crystal_treatment ; Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection. ; ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn.details ; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per min. Background counts for 5 sec on each side every scan. ; _diffrn.ambient_temperature 293 ;
save_diffrn.ambient_environment.
_item_description.description ; The gas or liquid surrounding the sample, if not air or vacuum. ; _item.name '_diffrn.ambient_environment' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The pressure in kilopascals at which the diffraction data were measured. ; _item.name '_diffrn.ambient_pressure' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_pressure' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'kilopascals'
save_diffrn.ambient_pressure_esd.
_item_description.description ; The estimated standard deviation of _diffrn.ambient_pressure. ; _item.name '_diffrn.ambient_pressure_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kilopascals'
save_diffrn.ambient_temperature.
_item_description.description ; The mean temperature in degrees Kelvin at which the diffraction data were measured. ; _item.name '_diffrn.ambient_temperature' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_temperature' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'kelvin'
save_diffrn.ambient_temperature_esd.
_item_description.description ; The estimated standard deviation of _diffrn.ambient_temperature. ; _item.name '_diffrn.ambient_temperature_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kelvin'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The physical device used to support the crystal during data collection. ; _item.name '_diffrn.crystal_support' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'glass capillary' 'quartz capillary' 'fiber' 'metal loop'
save_diffrn.crystal_treatment.
_item_description.description ; Remarks about how the crystal was treated prior to data collection. Particularly relevant when data were measured at low temperature. ; _item.name '_diffrn.crystal_treatment' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'equilibrated in hutch for 24 hours' 'flash frozen in liquid nitrogen' 'slow cooled with direct air stream'
_item_description.description ; Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. ; _item.name '_diffrn.details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_special_details' _item_type.code char
_category.description ; Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_attenuator.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _diffrn_attenuator.code _diffrn_attenuator.scale 1 16.976 ;
_item_description.description ; A code associated with a particular attenuator setting. This code is referenced by the _diffrn_refln.attenuator_code which is stored with the diffraction data. See _diffrn_attenuator.scale. ; _item.name '_diffrn_attenuator.code' _item.category_id _item.category_id _item.mandatory_code yes _item_aliases.alias_name '_diffrn_attenuator_code' _item_type.code char
_item_description.description ; The intensity scale associated with a particular attenuator setting identified by _diffrn_attenuator.code. ; _item.name '_diffrn_attenuator.scale' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_attenuator_scale' _item_range.maximum ? _item_range.minimum 1.0 _item_type.code float
_category.description ; Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_measurement.block_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _diffrn_measurement.device_type '3-circle camera' _diffrn_measurement.device_specific 'Supper model x' _diffrn_measurement.device_details 'none' _diffrn_measurement.method 'omega scan' _diffrn_measurement.details ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn_measurement.device 'Philips PW1100/20 diffractometer' _diffrn_measurement.method \q/2\q ;
save_diffrn_measurement.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_measurement.details.
_item_description.description ; A description of special aspects of the data measurement. ; _item.name '_diffrn_measurement.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ;
save_diffrn_measurement.device.
_item_description.description ; Description of the diffractometer or camera used to measure the diffraction intensities. ; _item.name '_diffrn_measurement.device' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device' _item_type.code char _item_examples.case 'Gandolfi 114mm powder camera'
save_diffrn_measurement.device_details.
_item_description.description ; A description of special aspects of the device used to measure the diffraction intensities. ; _item.name '_diffrn_measurement.device_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Need new example here. ;
save_diffrn_measurement.device_specific.
_item_description.description ; The particular device used to measure the diffraction intensities. In general this will be a manufacturer, description, model number of some combination of these.r ; _item.name '_diffrn_measurement.device_specific' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Supper model q' 'Huber model r' 'Enraf-Nonius model s' 'homemade'
save_diffrn_measurement.device_type.
_item_description.description ; The general class of the device used to measure the diffraction intensities. ; _item.name '_diffrn_measurement.device_type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '3-circle camera' '4-circle camera' 'kappa-geometry camera' 'oscillation camera' 'precession camera'
save_diffrn_measurement.method.
_item_description.description ; Method used to measure diffraction data. ; _item.name '_diffrn_measurement.method' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_method' _item_type.code char _item_examples.case 'profile data from theta/2theta scans'
_category.description ; Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in data measurement. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_orient_matrix.block_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on ; ; Need Example 2 ;
save_diffrn_orient_matrix.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_orient_matrix.type.
_item_description.description ; A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. ; _item.name '_diffrn_orient_matrix.type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_type' _item_type.code char
_item_description.description ; The elements of the diffractometer orientation matrix. These define the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB' _item.category_id _item.category_id _item.mandatory_code no _item_structure.code 'matrix3x3' _item_structure.organization 'rowwise' _item_type.code float
save_diffrn_orient_matrix.UB[1][1].
_item_description.description ; The [1][1] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[1][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_11' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[1][2].
_item_description.description ; The [1][2] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[1][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_12' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[1][3].
_item_description.description ; The [1][3] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[1][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_13' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[2][1].
_item_description.description ; The [2][1] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[2][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_21' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[2][2].
_item_description.description ; The [2][2] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[2][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_22' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[2][3].
_item_description.description ; The [2][3] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[2][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_23' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[3][1].
_item_description.description ; The [3][1] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[3][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_31' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[3][2].
_item_description.description ; The [3][2] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[3][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_32' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_orient_matrix.UB[3][3].
_item_description.description ; The [3][3] element of the 3x3 matrix _diffrn_orient_matrix.UB. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_orient_matrix.UB[3][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_33' _item_related.related_name '_diffrn_orient_matrix.UB' _item_related.function_code 'alternative_exclusive' _item_type.code float
_category.description ; Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in measurement of diffraction intensities. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_k' '_diffrn_orient_refln.index_l' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on ; ; Need Example 2 ;
save_diffrn_orient_refln.angle_chi.
_item_description.description ; Diffractometer angle chi in degrees of a reflection used to define the orientation matrix. See _diffrn_orient_matrix.UB and the Miller indices in the DIFFRN_ORIENT_RELFN category. ; _item.name '_diffrn_orient_refln.angle_chi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_chi' loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' _item_type.code float _item_units.code 'degrees'
save_diffrn_orient_refln.angle_kappa.
_item_description.description ; Diffractometer angle kappa in degrees of a reflection used to define the orientation matrix. See _diffrn_orient_matrix.UB and the Miller indices in the DIFFRN_ORIENT_RELFN category. ; _item.name '_diffrn_orient_refln.angle_kappa' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_kappa' loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' _item_type.code float _item_units.code 'degrees'
save_diffrn_orient_refln.angle_phi.
_item_description.description ; Diffractometer angle phi in degrees of a reflection used to define the orientation matrix. See _diffrn_orient_matrix.UB and the Miller indices in the DIFFRN_ORIENT_RELFN category. ; _item.name '_diffrn_orient_refln.angle_phi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_phi' loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_psi' _item_type.code float _item_units.code 'degrees'
save_diffrn_orient_refln.angle_psi.
_item_description.description ; Diffractometer angle psi in degrees of a reflection used to define the orientation matrix. See _diffrn_orient_matrix.UB and the Miller indices in the DIFFRN_ORIENT_RELFN category. ; _item.name '_diffrn_orient_refln.angle_psi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_psi' loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_phi' _item_type.code float _item_units.code 'degrees'
save_diffrn_orient_refln.index_h.
_item_description.description ; Miller index h of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_orient_refln_index_h' loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_k' '_diffrn_orient_refln.index_l' _item_type.code int
save_diffrn_orient_refln.index_k.
_item_description.description ; Miller index k of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_orient_refln_index_k' loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_l' _item_type.code int
save_diffrn_orient_refln.index_l.
_item_description.description ; Miller index l of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_orient_refln_index_l' loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_l' _item_type.code int
_category.description ; Data items in the DIFFRN_RADIATION category record details about the radiation and detector used in measuring diffraction intensities. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_radiation.block_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _diffrn_radiation.detector_type 'multiwire' _diffrn_radiation.detector_specific 'Siemens' _diffrn_radiation.source_type 'rotating anode' _diffrn_radiation.source_specific 'Rigaku RU-200' _diffrn_radiation.source_power '50 kw, 180 mA' _diffrn_radiation.source_target '8mm x 0.4 mm broad-focus' _diffrn_radiation.collimation '0.3 mm double pinhole' _diffrn_radiation.monochromator 'graphite' _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.wavelength 1.54 ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn_radiation.wavelength 1.5418 _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.monochromator 'graphite' _diffrn_radiation.source 'X-ray tube' ;
save_diffrn_radiation.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_radiation.collimation.
_item_description.description ; The collimation or focusing applied to the radiation. ; _item.name '_diffrn_radiation.collimation' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors'
save_diffrn_radiation.detector.
_item_description.description ; The detector used to measure the diffraction intensities. ; _item.name '_diffrn_radiation.detector' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_detector' _item_type.code char loop_ _item_examples.case 'scintillation' 'LiI' 'video tube' 'Kodak II film'
save_diffrn_radiation.detector_dtime.
_item_description.description ; The deadtime in microseconds of _diffrn_radiation.detector. ; _item.name '_diffrn_radiation.detector_dtime' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_detector_dtime' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'microseconds'
save_diffrn_radiation.detector_specific.
_item_description.description ; The particular radiation detector. In general this will be a manufacturer, description, model number or some combination of these. ; _item.name '_diffrn_radiation.detector_specific' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Siemens model x' 'Kodak XG' 'MAR Research model y'
save_diffrn_radiation.detector_type.
_item_description.description ; The general class of the radiation detector. ; _item.name '_diffrn_radiation.detector_type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'multiwire' 'imaging plate' 'CCD' 'film'
save_diffrn_radiation.filter_edge.
_item_description.description ; Absorption edge of the radiation filter used. ; _item.name '_diffrn_radiation.filter_edge' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_filter_edge' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_diffrn_radiation.inhomogeneity.
_item_description.description ; Half-width in millimetres of the incident beam in the perpendic- ular direction with respect to the diffraction plane. ; _item.name '_diffrn_radiation.inhomogeneity' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_inhomogeneity' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'millimetres'
save_diffrn_radiation.monochromator.
_item_description.description ; The method used to obtain monochromatic radiation. If a mono- chromator crystal is used the material and the indices of the Bragg reflection are specified. ; _item.name '_diffrn_radiation.monochromator' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_monochromator' _item_type.code char loop_ _item_examples.case 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite'
save_diffrn_radiation.polarisn_norm.
_item_description.description ; The angle in degrees of the perpendicular polarisation component to the diffraction plane. See _diffrn_radiation.polarisn_ratio. ; _item.name '_diffrn_radiation.polarisn_norm' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_norm' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_radiation.polarisn_ratio.
_item_description.description ; Polarisation ratio of the diffraction beam incident on the crystal. It is the ratio of the perpendicularly polarised to the parallel polarised component of the radiation. The perpendicular component forms an angle of _diffrn_radiation.polarisn_norm to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). ; _item.name '_diffrn_radiation.polarisn_ratio' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_ratio' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description ; The source of radiation. ; _item.name '_diffrn_radiation.source' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_source' _item_type.code char loop_ _item_examples.case 'RU2 Rigaku Denki rotating Cu anode' 'fine focus Philips Mo tube' '5MeV synchrotron' 'HIFAR reactor'
save_diffrn_radiation.source_details.
_item_description.description ; A description of special aspects of the source of radiation. ; _item.name '_diffrn_radiation.source_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Need new example here. ;
save_diffrn_radiation.source_power.
_item_description.description ; The power of the radiation source. ; _item.name '_diffrn_radiation.source_power' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '50 kV, 35 mA' '8 kW' '12 GeV'
save_diffrn_radiation.source_specific.
_item_description.description ; The particular source of radiation. In general this will be a manufacturer, description, or model number (or some combination of these) for laboratory sources and an institution name and beamline name for synchrotron sources. ; _item.name '_diffrn_radiation.source_specific' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Rigaku RU200' 'Philips fine focus Mo' 'NSLS beamline X8C'
save_diffrn_radiation.source_target.
_item_description.description ; The nature of the cathode target of the radiation source. ; _item.name '_diffrn_radiation.source_target' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '8mm x 0.4 mm fine-focus' 'broad focus'
save_diffrn_radiation.source_type.
_item_description.description ; The general class of the source of radiation. ; _item.name '_diffrn_radiation.source_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_source_type' _item_type.code char loop_ _item_examples.case 'sealed tube' 'rotating anode' 'synchrotron'
_item_description.description ; The nature of the radiation. ; _item.name '_diffrn_radiation.type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case CuK\a neutron electron
save_diffrn_radiation.wavelength.
_item_description.description ; The radiation wavelength. ; _item.name '_diffrn_radiation.wavelength' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_wavelength' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_diffrn_radiation.wavelength_id.
_item_description.description ; The code identifying each value of _diffrn_radiation.wavelength. Items in the the DIFFRN_RADIATION category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN list. It must match with one of the _diffrn_refln.wavelength_id codes. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_radiation.wavelength_id' diffrn_radiation yes '_diffrn_refln.wavelength_id' diffrn_refln yes '_refln.wavelength_id' refln yes _item_aliases.alias_name '_diffrn_radiation_wavelength_id' loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.wavelength_id' '_diffrn_radiation.wavelength_id' '_refln.wavelength_id' '_diffrn_radiation.wavelength_id' loop_ _item_type.code char loop_ _item_examples.case x1 x2 neut
save_diffrn_radiation.wavelength_wt.
_item_description.description ; The relative weight of a wavelength identified by the code _diffrn_radiation.wavelength_id in the list of wavelengths. ; _item.name '_diffrn_radiation.wavelength_wt' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_wavelength_wt' _item_default.value 1.0 _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
save_diffrn_radiation_detector_details.
_item_description.description ; A description of special aspects of the radiation detector. ; _item.name '_diffrn_radiation.detector_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Need new example here. ;
_category.description ; Data items in the DIFFRN_REFLN category record details about the intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements, and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements. The DIFFRN_REFLN data items are not looped. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_refln.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on ; ; Need Example 2 ;
_item_description.description ; The diffractometer angle chi in degrees of a reflection. This angle corresponds correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_chi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_chi' _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.angle_kappa.
_item_description.description ; The diffractometer angle kappa in degrees of a reflection. This angle corresponds correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_kappa' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_kappa' _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.angle_omega.
_item_description.description ; The diffractometer angle omega in degrees of a reflection. This angle corresponds correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_omega' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_omega' _item_type.code float _item_units.code 'degrees'
_item_description.description ; The diffractometer angle phi in degrees of a reflection. This angle corresponds correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_phi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_phi' _item_type.code float _item_units.code 'degrees'
_item_description.description ; The diffractometer angle psi in degrees of a reflection. This angle corresponds correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_psi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_psi' _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.angle_theta.
_item_description.description ; The diffractometer angle theta in degrees of a reflection. This angle corresponds correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_theta' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_theta' _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.attenuator_code.
_item_description.description ; The code identifying the attenuator setting for this reflection. This code must match one of the _diffrn.attenuator_code values. ; _item.name '_diffrn_refln.attenuator_code' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_attenuator_code' _item_type.code char
save_diffrn_refln.counts_bg_1.
_item_description.description ; The diffractometer counts for the measurement of the background before the peak. ; _item.name '_diffrn_refln.counts_bg_1' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_bg_1' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_refln.counts_bg_2.
_item_description.description ; The diffractometer counts for the measurement of the background background after the peak. ; _item.name '_diffrn_refln.counts_bg_2' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_bg_2' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_item_description.description ; The diffractometer counts for the measurement of net counts after background removal. ; _item.name '_diffrn_refln.counts_net' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_net' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_refln.counts_peak.
_item_description.description ; The diffractometer counts for the measurement of counts for the peak scan or position. ; _item.name '_diffrn_refln.counts_peak' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_peak' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_refln.counts_total.
_item_description.description ; The diffractometer counts for the measurement of total counts (background plus peak). ; _item.name '_diffrn_refln.counts_total' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_total' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_refln.detect_slit_horiz.
_item_description.description ; Total horizontal slit apertures in degrees. ; _item.name '_diffrn_refln.detect_slit_horiz' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_horiz' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.detect_slit_vert.
_item_description.description ; Total vertical slit apertures in degrees. ; _item.name '_diffrn_refln.detect_slit_vert' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_vert' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.elapsed_time.
_item_description.description ; Elapsed time in minutes from the start of diffraction measurement to the measurement of this intensity. ; _item.name '_diffrn_refln.elapsed_time' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_elapsed_time' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'minutes'
_item_description.description ; The value of diffrn_refln.id must uniquely identify a record in the DIFFRN_REFLN category. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_diffrn_refln.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
_item_description.description ; Miller index h of a diffraction reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Millder indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are described in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix. ; _item.name '_diffrn_refln.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_refln_index_h' loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_k' _item_type.code int
_item_description.description ; Miller index k of a diffraction reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Millder indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are described in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix. ; _item.name '_diffrn_refln.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_refln_index_k' loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_l' _item_type.code int
_item_description.description ; Miller index l of a diffraction reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Millder indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are described in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix. ; _item.name '_diffrn_refln.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_refln_index_l' loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_k' _item_type.code int
save_diffrn_refln.intensity_net.
_item_description.description ; Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_net' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_intensity_net' _item_range.maximum ? _item_range.minimum 0 _item_type.code float
save_diffrn_refln.intensity_sigma.
_item_description.description ; E.s.d. of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_sigma' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_intensity_sigma' _item_range.maximum ? _item_range.minimum 0 _item_type.code float
_item_description.description ; The code identifying the mode of scanning with a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. ; _item.name '_diffrn_refln.scan_mode' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_mode' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail om 'omega scan' ot 'omega/2theta scan'
save_diffrn_refln.scan_mode_backgd.
_item_description.description ; The code identifying the mode of scanning a reflection to measure the background intensity. ; _item.name '_diffrn_refln.scan_mode_backgd' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_mode_backgd' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail st 'stationary counter background' mo 'moving counter background'
_item_description.description ; The scan width in degrees of the scan mode defined by the code _diffrn_refln.scan_mode. ; _item.name '_diffrn_refln.scan_width' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_width' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.sint/lambda.
_item_description.description ; The sine theta over wavelength value for this reflection. ; _item.name '_diffrn_refln.sint/lambda' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_sint/lambda' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'reciprocal_angstroms'
_item_description.description ; The mean wavelength of radiation used to measure diffraction for this reflection. This is an important parameter for data collected using energy dispersive detectors or the Laue method. ; _item.name '_diffrn_refln.wavelength' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_wavelength' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_diffrn_refln.wavelength_id.
_item_description.description ; This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category. ; _item_aliases.alias_name '_diffrn_refln_wavelength_id'
_category.description ; Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements, and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements. The DIFFRN_REFLN data items are not looped. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_reflns.block_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn_reflns.number 1592 _diffrn_reflns.av_R_equivalents 0 _diffrn_reflns.av_sigmaI/netI .027 _diffrn_reflns.limit_h_min 0 _diffrn_reflns.limit_h_max 6 _diffrn_reflns.limit_k_min -17 _diffrn_reflns.limit_k_max 0 _diffrn_reflns.limit_l_min 0 _diffrn_reflns.limit_l_max 22 _diffrn_reflns.theta_min 3.71 _diffrn_reflns.theta_max 61.97 ;
save_diffrn_reflns.av_R_equivalents.
_item_description.description ; The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average difference between av(I) and the individual intensities. ; _item.name '_diffrn_reflns.av_R_equivalents' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_av_R_equivalents' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_diffrn_reflns.av_sigmaI/netI.
_item_description.description ; Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. ; _item.name '_diffrn_reflns.av_sigmaI/netI' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_av_sigmaI/netI' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_reflns.limit_h_max.
_item_description.description ; The maximum value of the diffraction reflection data specified by _diffrn_refln.index_h. ; _item.name '_diffrn_reflns.limit_h_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_h_max' _item_type.code int
save_diffrn_reflns.limit_h_min.
_item_description.description ; The minimum value of the diffraction reflection data specified by _diffrn_refln.index_h. ; _item.name '_diffrn_reflns.limit_h_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_h_min' _item_type.code int
save_diffrn_reflns.limit_k_max.
_item_description.description ; The maximum value of the diffraction reflection data specified by _diffrn_refln.index_k. ; _item.name '_diffrn_reflns.limit_k_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_k_max' _item_type.code int
save_diffrn_reflns.limit_k_min.
_item_description.description ; The minimum value of the diffraction reflection data specified by _diffrn_refln.index_k. ; _item.name '_diffrn_reflns.limit_k_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_k_min' _item_type.code int
save_diffrn_reflns.limit_l_max.
_item_description.description ; The maximum value of the diffraction reflection data specified by _diffrn_refln.index_l. ; _item.name '_diffrn_reflns.limit_l_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_l_max' _item_type.code int
save_diffrn_reflns.limit_l_min.
_item_description.description ; The minimum value of the diffraction reflection data specified by _diffrn_refln.index_l. ; _item.name '_diffrn_reflns.limit_l_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_l_min' _item_type.code int
_item_description.description ; The total number of measured diffraction data. ; _item.name '_diffrn_reflns.number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_number' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_reflns.reduction_process.
_item_description.description ; A description of the process used to reduce the intensity data into structure-factor magnitudes. ; _item.name '_diffrn_reflns.reduction_process' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_reduction_process' _item_type.code char _item_examples.case 'data averaged using Fisher test'
_item_description.description ; Maximum theta angle in degrees for the measured diffraction data. ; _item.name '_diffrn_reflns.theta_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_max' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
_item_description.description ; Minimum theta angle in degrees for the measured diffraction data. ; _item.name '_diffrn_reflns.theta_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_min' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_reflns.transf_matrix.
_item_description.description ; The matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. |11 12 13| (h k l) diffraction |21 22 23| = (h' k' l') |31 32 33| ; _item.name '_diffrn_reflns.transf_matrix' _item.category_id _item.category_id _item.mandatory_code no _item_structure.code 'matrix3x3' _item_structure.organization 'rowwise' _item_type.code float
save_diffrn_reflns.transf_matrix[1][1].
_item_description.description ; The [1][1] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[1][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_11' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[1][2].
_item_description.description ; The [1][2] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[1][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_12' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[1][3].
_item_description.description ; The [1][3] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[1][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_13' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[2][1].
_item_description.description ; The [2][1] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[2][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_21' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[2][2].
_item_description.description ; The [2][2] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[2][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_22' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[2][3].
_item_description.description ; The [2][3] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[2][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_23' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[3][1].
_item_description.description ; The [3][1] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[3][1]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_31' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[3][2].
_item_description.description ; The [3][2] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[3][2]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_32' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
save_diffrn_reflns.transf_matrix[3][3].
_item_description.description ; The [3][3] element of the 3x3 matrix _diffrn_reflns.transf_matrix. This data item is only present in this dictionary for compliance (via the alias) with previous dictionaries. ; _item.name '_diffrn_reflns.transf_matrix[3][3]' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_33' _item_related.related_name '_diffrn_reflns.transf_matrix' _item_related.function_code 'alternative_exclusive' _item_type.code float
_category.description ; Data items in the DIFFRN_SCALE_GROUP category record details about the reflections used to scale the diffraction intensities. Scaling groups might, for instance, correspond to each film in a multi-film data set, or each crystal in a mutli-crystal data set. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_scale_group.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on ; ; Need Example 2 ;
_item_description.description ; The value of diffrn_scale_group.code must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_scale_group.code' diffrn_scale_group yes '_diffrn_refln.scale_group_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_scale_group_code' loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.scale_group_code' '_diffrn_scale_group.code' _item_type.code char loop_ _item_examples.case 1 2 3 s1 A B c1 c2 c3
_item_description.description ; The value of diffrn_scale_group.code must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_scale_group.code' diffrn_scale_group yes '_diffrn_refln.scale_group_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_scale_group_code' loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.scale_group_code' '_diffrn_scale_group.code' _item_type.code char loop_ _item_examples.case 1 2 3 s1 A B c1 c2 c3
save_diffrn_scale_group.I_net.
_item_description.description ; The scale for a specific measurement group which is to multiplied with the net intensity to place all intensities in the _diffrn_refln. or REFLN list on a common scale. ; _item.name '_diffrn_scale_group.I_net' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_scale_group_I_net' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_category.description ; Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_standard_refln.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _diffrn_standard_refln.index_h _diffrn_standard_refln.index_k _diffrn_standard_refln.index_l 3 2 4 1 9 1 3 0 10 ;
save_diffrn_standard_refln.code.
_item_description.description ; The code identifying a reflection measured as a standard reflection with the indices _diffrn_standard_refln.index_. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_standard_refln.code' diffrn_standard_refln yes '_diffrn_refln.standard_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_standard_refln_code' loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.standard_code' '_diffrn_standard_refln.code' _item_type.code char loop_ _item_examples.case 1 2 3 s1 A B
save_diffrn_standard_refln.code.
_item_description.description ; The code identifying a reflection measured as a standard reflection with the indices _diffrn_standard_refln.index_. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_standard_refln.code' diffrn_standard_refln yes '_diffrn_refln.standard_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_standard_refln_code' loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.standard_code' '_diffrn_standard_refln.code' _item_type.code char loop_ _item_examples.case 1 2 3 s1 A B
save_diffrn_standard_refln.index_h.
_item_description.description ; Miller index h of a standard reflection used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_standard_refln_index_h' loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_k' '_diffrn_standard_refln.index_l' _item_type.code int
save_diffrn_standard_refln.index_k.
_item_description.description ; Miller index k of a standard reflections used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_standard_refln_index_k' loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_h' '_diffrn_standard_refln.index_l' _item_type.code int
save_diffrn_standard_refln.index_l.
_item_description.description ; Miller index l of a standard reflections used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_diffrn_standard_refln_index_l' loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_h' '_diffrn_standard_refln.index_k' _item_type.code int
_category.description ; Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. ; _category.id _category.id _category.mandatory_code no _category_key.name '_diffrn_standards.block_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn_standards.number 3 _diffrn_standards.interval_time 120 _diffrn_standards.decay_% 0 ;
save_diffrn_standards.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_standards.decay_%.
_item_description.description ; The percentage variation of the mean intensity for all standard reflections. ; _item.name '_diffrn_standards.decay_%' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_decay_%' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_diffrn_standards.interval_count.
_item_description.description ; The number of reflection intensities between the measurement of standard reflection intensities. ; _item.name '_diffrn_standards.interval_count' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_interval_count' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_standards.interval_time.
_item_description.description ; The time in minutes between the measurement of standard reflection intensities. ; _item.name '_diffrn_standards.interval_time' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_interval_time' _item_range.maximum ? _item_range.minimum 0 _item_type.code float _item_units.code 'minutes'
_item_description.description ; The number of unique standard reflections used in the diffraction measurements. ; _item.name '_diffrn_standards.number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_number' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_standards.scale_sigma.
_item_description.description ; The e.s.d. of the individual mean standard scales applied to the intensity data. ; _item.name '_diffrn_standards.scale_sigma' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_scale_sigma' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_category.description ; Data items in the ENTITY category record details (such as chemical composition, name, and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY sub-categories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications, and replaces the function of the _chemical. data items in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented in the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation, and can most usefully be though of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity.id _entity.type _entity.formula_weight _entity.details 1 polymer 10916 ; The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer. ; 2 non-polymer 'need number here' '.' 3 water 18 '.' ;
_item_description.description ; A description of special aspects of the entity. ; _item.name '_entity.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; Formula mass in daltons of the entity. ; _item.name '_entity.formula_weight' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 1.0 _item_type.code float
_item_description.description ; The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity.id' entity yes '_atom_site.entity_id' atom_site yes '_entity_keywords.entity_id' entity_keywords yes '_entity_name_com.entity_id' entity_name_com yes '_entity_name_sys.entity_id' entity_name_sys yes '_entity_poly.entity_id' entity_poly yes '_entity_poly_seq.entity_id' entity_poly_seq yes '_entity_poly_seq_dif.entity_id' entity_poly_seq_dif yes '_entity_reference.entity_id' entity_reference yes '_entity_src_gen.entity_id' entity_src_gen yes '_entity_src_nat.entity_id' entity_src_nat yes '_struct_asym.entity_id' struct_asym yes _item_type.code char loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.entity_id' '_entity.id' '_entity_keywords.entity_id' '_entity.id' '_entity_name_com.entity_id' '_entity.id' '_entity_name_sys.entity_id' '_entity.id' '_entity_poly.entity_id' '_entity.id' '_entity_poly_seq.entity_id' '_entity_poly.entity_id' '_entity_poly_seq_dif.entity_id' '_entity_poly_seq.entity_id' '_entity_reference.entity_id' '_entity.id' '_entity_src_gen.entity_id' '_entity.id' '_entity_src_nat.entity_id' '_entity.id' '_struct_asym.entity_id' '_entity.id'
_item_description.description ; The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity.id' entity yes '_atom_site.entity_id' atom_site yes '_entity_keywords.entity_id' entity_keywords yes '_entity_name_com.entity_id' entity_name_com yes '_entity_name_sys.entity_id' entity_name_sys yes '_entity_poly.entity_id' entity_poly yes '_entity_poly_seq.entity_id' entity_poly_seq yes '_entity_poly_seq_dif.entity_id' entity_poly_seq_dif yes '_entity_reference.entity_id' entity_reference yes '_entity_src_gen.entity_id' entity_src_gen yes '_entity_src_nat.entity_id' entity_src_nat yes '_struct_asym.entity_id' struct_asym yes _item_type.code char loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.entity_id' '_entity.id' '_entity_keywords.entity_id' '_entity.id' '_entity_name_com.entity_id' '_entity.id' '_entity_name_sys.entity_id' '_entity.id' '_entity_poly.entity_id' '_entity.id' '_entity_poly_seq.entity_id' '_entity_poly.entity_id' '_entity_poly_seq_dif.entity_id' '_entity_poly_seq.entity_id' '_entity_reference.entity_id' '_entity.id' '_entity_src_gen.entity_id' '_entity.id' '_entity_src_nat.entity_id' '_entity.id' '_struct_asym.entity_id' '_entity.id'
_item_description.description ; The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples, etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. ; _item.name '_entity.src_method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail nat 'entity was isolated from a natural source' man ; entity was isolated from a genetically manipulated source ;
_item_description.description ; Defines the type of the entity. Polymer entities will be expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities will be expected to have corresponding ENTITY_NPOL and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. ; _item.name '_entity.type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail polymer 'entity is a polymer' non-polymer 'entity is not a polymer' water 'water in the solvent model'
_category.description ; Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used to keyword the STRUCT_BIOL data items, and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, and not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, and not transfer- RNA. ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_keywords.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_keywords.entity_id _entity_keywords.text 1 'polypeptide' 2 'natural product' 2 'inhibitor' 2 'reduced peptide' ;
save_entity_keywords.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; Keywords describing this entity. ; _item.name '_entity_keywords.text' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'polypeptide' 'natural product' 'polysaccharide'
_category.description ; Data items in the ENTITY_LINK category give details about the linkages between monomers in a polymer. ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_link.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; Need Example 1 ;
_item_description.description ; A description of special aspects of a linkage between monomers in a polymer. ; _item.name '_entity_link.model_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The value of _entity_link.id must uniquely identify each item in the ENTITY_LINK list. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_link.id' entity_link yes '_entity_link_angle.link_id' entity_link_angle yes '_entity_link_bond.link_id' entity_link_bond yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_link_angle.link_id' '_entity_link.id' '_entity_link_bond.link_id' '_entity_link.id' _item_type.code char loop_ _item_examples.case 'peptide' 'oligosaccharide 1,4' 'DNA'
_item_description.description ; The value of _entity_link.id must uniquely identify each item in the ENTITY_LINK list. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_link.id' entity_link yes '_entity_link_angle.link_id' entity_link_angle yes '_entity_link_bond.link_id' entity_link_bond yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_link_angle.link_id' '_entity_link.id' '_entity_link_bond.link_id' '_entity_link.id' _item_type.code char loop_ _item_examples.case 'peptide' 'oligosaccharide 1,4' 'DNA'
_item_description.description ; The value of _entity_link.id must uniquely identify each item in the ENTITY_LINK list. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_link.id' entity_link yes '_entity_link_angle.link_id' entity_link_angle yes '_entity_link_bond.link_id' entity_link_bond yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_link_angle.link_id' '_entity_link.id' '_entity_link_bond.link_id' '_entity_link.id' _item_type.code char loop_ _item_examples.case 'peptide' 'oligosaccharide 1,4' 'DNA'
_item_description.description ; The type of the second of the two monomers joined by the linkage. This data item is a pointer to _entity_mon.type in the ENTITY_MON category. ; _item.name '_entity_link.type_mon_1' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the ENTITY_LINK_ANGLE category record details about angles in a linkage between monomers in a polymer. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_link_angle.link_id' '_entity_link_angle.atom_id_1' '_entity_link_angle.atom_id_2' '_entity_link_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; Need Example 1 ;
save_entity_link_angle.atom_1_atom_id.
_item_description.description ; The id of the first of the three atoms that define the angle. As this data item does not point to a specific atom in a specific monomer, it is not a child in the linkage sense. ; _item.name '_entity_link_angle.atom_1_atom_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_angle.atom_2_atom_id' '_entity_link_angle.atom_3_atom_id' _item.mandatory_code no _item_type.code char
save_entity_link_angle.atom_1_mon_id.
_item_description.description ; This data item indiates whether atom 1 is found in the first or the second of the two monomers connected by the linkage. ; _item.name '_entity_link_angle.atom_1_mon_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_angle.atom_2_mon_id' '_entity_link_angle.atom_3_mon_id' _item.mandatory_code no loop_ _item_enumeration.code _item_enumeration.detail 1 'the atom is in monomer 1' 2 'the atom is in monomer 2'
save_entity_link_angle.atom_2_atom_id.
_item_description.description ; The id of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. As this data item does not point to a specific atom in a specific monomer, it is not a child in the linkage sense. ; _item.name '_entity_link_angle.atom_2_atom_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_angle.atom_1_atom_id' '_entity_link_angle.atom_3_atom_id' _item.mandatory_code no _item_type.code char
save_entity_link_angle.atom_2_mon_id.
_item_description.description ; This data item indiates whether atom 2 is found in the first or the second of the two monomers connected by the linkage. ; _item.name '_entity_link_angle.atom_2_mon_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_angle.atom_1_mon_id' '_entity_link_angle.atom_3_mon_id' _item.mandatory_code no loop_ _item_enumeration.code _item_enumeration.detail 1 'the atom is in monomer 1' 2 'the atom is in monomer 2'
save_entity_link_angle.atom_3_atom_id.
_item_description.description ; The id of the third of the three atoms that define the angle. As this data item does not point to a specific atom in a specific monomer, it is not a child in the linkage sense. ; _item.name '_entity_link_angle.atom_3_atom_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_angle.atom_1_atom_id' '_entity_link_angle.atom_2_atom_id' _item.mandatory_code no _item_type.code char
save_entity_link_angle.atom_3_mon_id.
_item_description.description ; This data item indiates whether atom 3 is found in the first or the second of the two monomers connected by the linkage. ; _item.name '_entity_link_angle.atom_3_mon_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_angle.atom_1_mon_id' '_entity_link_angle.atom_2_mon_id' _item.mandatory_code no loop_ _item_enumeration.code _item_enumeration.detail 1 'the atom is in monomer 1' 2 'the atom is in monomer 2'
save_entity_link_angle.value_angle.
_item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_entity_link_angle.value_angle' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum 180.0 _item_range.minimum 0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
save_entity_link_angle.value_angle_esd.
_item_description.description ; The estimated standard deviation of _entity_link_angle.value_angle. ; _item.name '_entity_link_angle.value_angle_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum 180.0 _item_range.minimum 0 _item_type.code float _item_units.code 'degrees'
save_entity_link_angle.value_dist.
_item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _entity_mon_angle.atom_id_1 and _entity_mon_angle.atom_id_3. ; _item.name '_entity_link_angle.value_dist' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_entity_link_angle.value_dist_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_angle.value_dist_esd. ; _item.name '_entity_link_angle.value_dist_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_category.description ; Data items in the ENTITY_LINK_BOND category record details about bonds in a linkage between monomers in a polymer. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_link_bond.link_id' '_entity_link_bond.atom_id_1' '_entity_link_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; Need Example 1 ;
save_entity_link_bond.atom_1_atom_id.
_item_description.description ; The id of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific monomer, it is not a child in the linkage sense. ; _item.name '_entity_link_bond.atom_1_atom_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_bond.atom_2_atom_id' _item.mandatory_code no _item_type.code char
save_entity_link_bond.atom_1_mon_id.
_item_description.description ; This data item indiates whether atom 1 is found in the first or the second of the two monomers connected by the linkage. ; _item.name '_entity_link_bond.atom_1_mon_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_bond.atom_2_mon_id' _item.mandatory_code no loop_ _item_enumeration.code _item_enumeration.detail 1 'the atom is in monomer 1' 2 'the atom is in monomer 2'
save_entity_link_bond.atom_2_atom_id.
_item_description.description ; The id of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific monomer, it is not a child in the linkage sense. ; _item.name '_entity_link_bond.atom_2_atom_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_bond.atom_1_atom_id' _item.mandatory_code no _item_type.code char
save_entity_link_bond.atom_2_mon_id.
_item_description.description ; This data item indiates whether atom 2 is found in the first or the second of the two monomers connected by the linkage. ; _item.name '_entity_link_bond.atom_2_mon_id' _item.category_id _item.category_id loop_ _item_dependent.dependent_name '_entity_link_bond.atom_1_mon_id' _item.mandatory_code no loop_ _item_enumeration.code _item_enumeration.detail 1 'the atom is in monomer 1' 2 'the atom is in monomer 2'
save_entity_link_bond.value_dist.
_item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_entity_link_bond.value_dist' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_entity_link_bond.value_dist_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_bond.value_dist_esd. ; _item.name '_entity_link_bond.value_dist_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_entity_link_bond.value_order.
_item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_entity_link_bond.value_order' _item.category_id _item.category_id _item.mandatory_code no _item_default.value sing _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalised double bond' pi 'pi bond'
_category.description ; Data items in the ENTITY_MON category give details (such as name, mass, charge, etc.) about each of the monomers from which the relevant polymers can be constructed. ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_mon.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon.id _entity_mon.model_source _entity_mon.name phe '1987 Protin/Prolsq Ideals file' phenylalanine val '1987 Protin/Prolsq Ideals file' alanine # - - - - data truncated for brevity - - - - ;
_item_description.description ; The value of _entity_mon.id must uniquely identify each item in the ENTITY_MON list. For protein polymer entities, this is the three-letter code for amino acids. For nucleic acid polymer entities, this is the one-letter code for the bases. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon.id' entity_mon yes '_atom_site.label_res_id' atom_site yes '_entity_mon_atom.mon_id' entity_mon_atom yes '_entity_mon_angle.mon_id' entity_mon_angle yes '_entity_mon_bond.mon_id' entity_mon_bond yes '_entity_mon_chir.mon_id' entity_mon_chir yes '_entity_mon_plane.mon_id' entity_mon_plane yes '_entity_mon_tor.mon_id' entity_mon_tor yes '_entity_poly_seq.mon_id' entity_poly_seq yes '_entity_poly_seq_dif.mon_id' entity_poly_seq_dif yes '_entity_poly_seq_dif.db_mon_id' entity_poly_seq_dif yes '_struct_conf.beg_label_res_id' struct_conf yes '_struct_conf.end_label_res_id' struct_conf yes '_struct_conn.ptnr1_label_res_id' struct_conn yes '_struct_conn.ptnr2_label_res_id' struct_conn yes '_struct_mon_nucl.label_res_id' struct_mon_nucl yes '_struct_mon_prot.label_res_id' struct_mon_prot yes '_struct_mon_prot_cis.label_res_id' struct_mon_prot_cis yes '_struct_ncs_dom_gen.beg_label_res_id' struct_ncs_dom_gen yes '_struct_ncs_dom_gen.end_label_res_id' struct_ncs_dom_gen yes '_struct_site_gen.label_res_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_res_id' '_entity_mon.id' '_entity_mon_atom.mon_id' '_entity_mon.id' '_entity_mon_chir.mon_id' '_entity_mon.id' '_entity_mon_plane.mon_id' '_entity_mon.id' '_entity_poly_seq.mon_id' '_entity_mon.id' '_entity_poly_seq_dif.db_mon_id' '_entity_mon.id' '_entity_mon_angle.mon_id' '_entity_mon_atom.mon_id' '_entity_mon_bond.mon_id' '_entity_mon_atom.mon_id' '_entity_mon_tor.mon_id' '_entity_mon_atom.mon_id' '_entity_poly_seq_dif.mon_id' '_entity_poly_seq.mon_id' '_struct_conf.beg_label_res_id' '_atom_site.label_res_id' '_struct_conf.end_label_res_id' '_atom_site.label_res_id' '_struct_conn.ptnr1_label_res_id' '_atom_site.label_res_id' '_struct_conn.ptnr2_label_res_id' '_atom_site.label_res_id' '_struct_mon_nucl.label_res_id' '_atom_site.label_res_id' '_struct_mon_prot.label_res_id' '_atom_site.label_res_id' '_struct_mon_prot_cis.label_res_id' '_atom_site.label_res_id' '_struct_ncs_dom_gen.beg_label_res_id' '_atom_site.label_res_id' '_struct_ncs_dom_gen.end_label_res_id' '_atom_site.label_res_id' '_struct_site_gen.label_res_id' '_atom_site.label_res_id' _item_type.code char loop_ _item_examples.case 'ala' 'val' 'A' 'C'
_item_description.description ; The value of _entity_mon.id must uniquely identify each item in the ENTITY_MON list. For protein polymer entities, this is the three-letter code for amino acids. For nucleic acid polymer entities, this is the one-letter code for the bases. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon.id' entity_mon yes '_atom_site.label_res_id' atom_site yes '_entity_mon_atom.mon_id' entity_mon_atom yes '_entity_mon_angle.mon_id' entity_mon_angle yes '_entity_mon_bond.mon_id' entity_mon_bond yes '_entity_mon_chir.mon_id' entity_mon_chir yes '_entity_mon_plane.mon_id' entity_mon_plane yes '_entity_mon_tor.mon_id' entity_mon_tor yes '_entity_poly_seq.mon_id' entity_poly_seq yes '_entity_poly_seq_dif.mon_id' entity_poly_seq_dif yes '_entity_poly_seq_dif.db_mon_id' entity_poly_seq_dif yes '_struct_conf.beg_label_res_id' struct_conf yes '_struct_conf.end_label_res_id' struct_conf yes '_struct_conn.ptnr1_label_res_id' struct_conn yes '_struct_conn.ptnr2_label_res_id' struct_conn yes '_struct_mon_nucl.label_res_id' struct_mon_nucl yes '_struct_mon_prot.label_res_id' struct_mon_prot yes '_struct_mon_prot_cis.label_res_id' struct_mon_prot_cis yes '_struct_ncs_dom_gen.beg_label_res_id' struct_ncs_dom_gen yes '_struct_ncs_dom_gen.end_label_res_id' struct_ncs_dom_gen yes '_struct_site_gen.label_res_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_res_id' '_entity_mon.id' '_entity_mon_atom.mon_id' '_entity_mon.id' '_entity_mon_chir.mon_id' '_entity_mon.id' '_entity_mon_plane.mon_id' '_entity_mon.id' '_entity_poly_seq.mon_id' '_entity_mon.id' '_entity_poly_seq_dif.db_mon_id' '_entity_mon.id' '_entity_mon_angle.mon_id' '_entity_mon_atom.mon_id' '_entity_mon_bond.mon_id' '_entity_mon_atom.mon_id' '_entity_mon_tor.mon_id' '_entity_mon_atom.mon_id' '_entity_poly_seq_dif.mon_id' '_entity_poly_seq.mon_id' '_struct_conf.beg_label_res_id' '_atom_site.label_res_id' '_struct_conf.end_label_res_id' '_atom_site.label_res_id' '_struct_conn.ptnr1_label_res_id' '_atom_site.label_res_id' '_struct_conn.ptnr2_label_res_id' '_atom_site.label_res_id' '_struct_mon_nucl.label_res_id' '_atom_site.label_res_id' '_struct_mon_prot.label_res_id' '_atom_site.label_res_id' '_struct_mon_prot_cis.label_res_id' '_atom_site.label_res_id' '_struct_ncs_dom_gen.beg_label_res_id' '_atom_site.label_res_id' '_struct_ncs_dom_gen.end_label_res_id' '_atom_site.label_res_id' '_struct_site_gen.label_res_id' '_atom_site.label_res_id' _item_type.code char loop_ _item_examples.case 'ala' 'val' 'A' 'C'
save_entity_mon.model_details.
_item_description.description ; A description of special aspects of the generation of the coordinates for the model of the monomer. ; _item.name '_entity_mon.model_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'geometry idealized but not minimized'
_item_description.description ; A pointer to an 'external reference file', if the atomic description of the monomer is taken from such a file. ; _item.name '_entity_mon.model_erf' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The source of the coordinates for the model of the non-polymer entity. ; _item.name '_entity_mon.model_source' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'CSD entry ABCDEF' 'built using Quanta/Charmm'
_item_description.description ; The full name of the monomer. ; _item.name '_entity_mon.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'alanine' 'valine' 'adenine' 'cytosine'
_item_description.description ; A description of the class of the non-standard monomer, if the group represents a modification of a standard monomer. ; _item.name '_entity_mon.nstd_class' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'iodinated base' 'phosporylated amino acid' 'bromined base' 'modified amino acid' 'glycosylated amino acid'
_item_description.description ; A description of special details of the non-standard monomer. ; _item.name '_entity_mon.nstd_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; 'yes' indicates that this is a "standard" monomer, 'no' that it is "non-standard." Non-standard monomers should be further described using the _entity_mon.nstd_parent, _entity_mon.nstd_class, and _entity_mon.nstd_details data items. ; _item.name '_entity_mon.nstd_flag' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value yes no
_item_description.description ; A name of the parent monomer of the non-standard monomer, if the group represents a modification of a standard monomer. ; _item.name '_entity_mon.nstd_parent' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'tyrosine' 'cytosine'
save_entity_mon.number_atoms_all.
_item_description.description ; The total number of atoms in the monomer. ; _item.name '_entity_mon.number_atoms_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon.number_atoms_nh.
_item_description.description ; The number of non-hydrogen atoms in the monomer. ; _item.name '_entity_mon.number_atoms_nh' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon.one_letter_code.
_item_description.description ; The one-letter code for the monomer. If there is not a standard one letter code for this monomer, or if this is a non-polymer monomer, the one-letter code should be given as 'X'. ; _item.name '_entity_mon.one_letter_code' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail A 'alanine' R 'arginine' N 'asparagine' D 'aspartic-acid' C 'cysteine' C 'cystine' Q 'glutamine' E 'glutamic-acid' G 'glycine' H 'histidine' I 'isoleucine' L 'leucine' K 'lysine' M 'methionine' F 'phenylalanine' P 'proline' S 'serine' T 'threonine' W 'tryptophan' Y 'tyrosine' V 'valine' A 'adenine' C 'cytosine' G 'guanine' T 'thymine' U 'uracil' O 'water' X 'other'
_item_description.description ; The type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap, and monomers with some type of C-terminal (or 3') cap. ; _item.name '_entity_mon.type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value 'D-peptide linking' 'L-peptide linking' 'D-peptide NH3 amino terminus' 'L-peptide NH3 amino terminus' 'D-peptide COOH carboxy terminus' 'L-peptide COOH carboxy terminus' 'DNA linking' 'RNA linking' 'DNA OH 5' terminus 'RNA OH 5' terminus 'DNA OH 3' terminus 'RNA OH 3' terminus 'D-saccharide 1,4 and 1,4 linking' 'L-saccharide 1,4 and 1,4 linking' 'D-saccharide 1,4 and 1,6 linking' 'L-saccharide 1,4 and 1,6 linking' 'non-polymer' 'other'
_category.description ; Data items in the ENTITY_MON_ANGLE category record details about angles in a monomer entity. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_angle.mon_id' '_entity_mon_angle.atom_id_1' '_entity_mon_angle.atom_id_2' '_entity_mon_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_angle.mon_id _entity_mon_angle.atom_id_1 _entity_mon_angle.atom_id_2 _entity_mon_angle.atom_id_3 _entity_mon_angle.value_angle _entity_mon_angle.value_dist phe N CA C xxx.xx x.xx phe CA C O xxx.xx x.xx phe CB CA C xxx.xx x.xx phe CB CA N xxx.xx x.xx phe CA CB CG xxx.xx x.xx phe CB CG CD1 xxx.xx x.xx phe CB CG CD2 xxx.xx x.xx phe CD1 CG CD2 xxx.xx x.xx phe CG CD1 CE1 xxx.xx x.xx phe CD1 CE1 CZ xxx.xx x.xx phe CE1 CZ CE2 xxx.xx x.xx phe CZ CE2 CD2 xxx.xx x.xx phe CG CD2 CE2 xxx.xx x.xx val N CA C xxx.xx x.xx val CA C O xxx.xx x.xx val CB CA C xxx.xx x.xx val CB CA N xxx.xx x.xx val CA CB CG1 xxx.xx x.xx val CA CB CG2 xxx.xx x.xx val CG1 CB CG2 xxx.xx x.xx ;
_item_description.description ; This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_entity_mon_angle.value_angle.
_item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_entity_mon_angle.value_angle' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum 180.0 _item_range.minimum 0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
save_entity_mon_angle.value_angle_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_angle.value_angle. ; _item.name '_entity_mon_angle.value_angle_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum 180.0 _item_range.minimum 0 _item_type.code float _item_units.code 'degrees'
save_entity_mon_angle.value_dist.
_item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _entity_mon_angle.atom_id_1 and _entity_mon_angle.atom_id_3. ; _item.name '_entity_mon_angle.value_dist' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_entity_mon_angle.value_dist_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_angle.value_dist_esd. ; _item.name '_entity_mon_angle.value_dist_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_category.description ; Data items in the ENTITY_MON_ATOM category record details about the atoms in a monomer entity. Atomic coordinates can be given for the monomer; specifying coordinates is an alternative to specifying the structure of the monomer via bonds, angles, planes, etc., in the appropriate ENTITY_MON subcategories. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_atom.mon_id' '_entity_mon_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_atom.mon_id _entity_mon_atom.atom_id _entity_mon_atom.type_symbol _entity_mon_atom.substruct_code _entity_mon_atom.model_cartn_x _entity_mon_atom.model_cartn_y _entity_mon_atom.model_cartn_z phe N N main 1.20134 0.84658 0.00000 phe CA C main 0.00000 0.00000 0.00000 phe C C main -1.25029 0.88107 0.00000 phe O O main -2.18525 0.66029 -0.78409 phe CB C side 0.00662 -1.03603 1.11081 phe CG C side 0.03254 -0.49711 2.50951 phe CD1 C side -1.15813 -0.12084 3.13467 phe CE1 C side -1.15720 0.38038 4.42732 phe CZ C side 0.05385 0.51332 5.11032 phe CE2 C side 1.26137 0.11613 4.50975 phe CD2 C side 1.23668 -0.38351 3.20288 val N N main 1.20134 0.84658 0.00000 val CA C main 0.00000 0.00000 0.00000 val C C main -1.25029 0.88107 0.00000 val O O main -2.18525 0.66029 -0.78409 val CB C side 0.05260 -0.99339 1.17429 val CG1 C side -0.13288 -0.31545 2.52668 val CG2 C side -0.94265 -2.12930 0.99811 ;
save_entity_mon_atom.alt_atom_id.
_item_description.description ; An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a monomer. ; _item.name '_entity_mon_atom.alt_atom_id' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The value of _entity_mon_atom.atom_id must uniquely identify each atom in each monomer in the ENTITY_MON_ATOM list. The atom identifiers need not be unique over all atoms in the CIF; they need only be unique for each atom in a monomer. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_atom.atom_id' entity_mon_atom yes '_atom_site.label_atom_id' atom_site yes '_entity_mon_angle.atom_id_1' entity_mon_angle yes '_entity_mon_angle.atom_id_2' entity_mon_angle yes '_entity_mon_angle.atom_id_3' entity_mon_angle yes '_entity_mon_bond.atom_id_1' entity_mon_bond yes '_entity_mon_bond.atom_id_2' entity_mon_bond yes '_entity_mon_chir.atom_id' entity_mon_chir yes '_entity_mon_chir_atom.atom_id' entity_mon_chir_atom yes '_entity_mon_plane_atom.atom_id' entity_mon_plane_atom yes '_entity_mon_tor.atom_id_1' entity_mon_tor yes '_entity_mon_tor.atom_id_2' entity_mon_tor yes '_entity_mon_tor.atom_id_3' entity_mon_tor yes '_entity_mon_tor.atom_id_4' entity_mon_tor yes '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_chir.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_chir_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_plane_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_4' '_entity_mon_atom.atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code char
_item_description.description ; The value of _entity_mon_atom.atom_id must uniquely identify each atom in each monomer in the ENTITY_MON_ATOM list. The atom identifiers need not be unique over all atoms in the CIF; they need only be unique for each atom in a monomer. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_atom.atom_id' entity_mon_atom yes '_atom_site.label_atom_id' atom_site yes '_entity_mon_angle.atom_id_1' entity_mon_angle yes '_entity_mon_angle.atom_id_2' entity_mon_angle yes '_entity_mon_angle.atom_id_3' entity_mon_angle yes '_entity_mon_bond.atom_id_1' entity_mon_bond yes '_entity_mon_bond.atom_id_2' entity_mon_bond yes '_entity_mon_chir.atom_id' entity_mon_chir yes '_entity_mon_chir_atom.atom_id' entity_mon_chir_atom yes '_entity_mon_plane_atom.atom_id' entity_mon_plane_atom yes '_entity_mon_tor.atom_id_1' entity_mon_tor yes '_entity_mon_tor.atom_id_2' entity_mon_tor yes '_entity_mon_tor.atom_id_3' entity_mon_tor yes '_entity_mon_tor.atom_id_4' entity_mon_tor yes '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_chir.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_chir_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_plane_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_4' '_entity_mon_atom.atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code char
_item_description.description ; The value of _entity_mon_atom.atom_id must uniquely identify each atom in each monomer in the ENTITY_MON_ATOM list. The atom identifiers need not be unique over all atoms in the CIF; they need only be unique for each atom in a monomer. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_atom.atom_id' entity_mon_atom yes '_atom_site.label_atom_id' atom_site yes '_entity_mon_angle.atom_id_1' entity_mon_angle yes '_entity_mon_angle.atom_id_2' entity_mon_angle yes '_entity_mon_angle.atom_id_3' entity_mon_angle yes '_entity_mon_bond.atom_id_1' entity_mon_bond yes '_entity_mon_bond.atom_id_2' entity_mon_bond yes '_entity_mon_chir.atom_id' entity_mon_chir yes '_entity_mon_chir_atom.atom_id' entity_mon_chir_atom yes '_entity_mon_plane_atom.atom_id' entity_mon_plane_atom yes '_entity_mon_tor.atom_id_1' entity_mon_tor yes '_entity_mon_tor.atom_id_2' entity_mon_tor yes '_entity_mon_tor.atom_id_3' entity_mon_tor yes '_entity_mon_tor.atom_id_4' entity_mon_tor yes '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_chir.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_chir_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_plane_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_4' '_entity_mon_atom.atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code char
_item_description.description ; The value of _entity_mon_atom.atom_id must uniquely identify each atom in each monomer in the ENTITY_MON_ATOM list. The atom identifiers need not be unique over all atoms in the CIF; they need only be unique for each atom in a monomer. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_atom.atom_id' entity_mon_atom yes '_atom_site.label_atom_id' atom_site yes '_entity_mon_angle.atom_id_1' entity_mon_angle yes '_entity_mon_angle.atom_id_2' entity_mon_angle yes '_entity_mon_angle.atom_id_3' entity_mon_angle yes '_entity_mon_bond.atom_id_1' entity_mon_bond yes '_entity_mon_bond.atom_id_2' entity_mon_bond yes '_entity_mon_chir.atom_id' entity_mon_chir yes '_entity_mon_chir_atom.atom_id' entity_mon_chir_atom yes '_entity_mon_plane_atom.atom_id' entity_mon_plane_atom yes '_entity_mon_tor.atom_id_1' entity_mon_tor yes '_entity_mon_tor.atom_id_2' entity_mon_tor yes '_entity_mon_tor.atom_id_3' entity_mon_tor yes '_entity_mon_tor.atom_id_4' entity_mon_tor yes '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_chir.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_chir_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_plane_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_4' '_entity_mon_atom.atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code char
_item_description.description ; The value of _entity_mon_atom.atom_id must uniquely identify each atom in each monomer in the ENTITY_MON_ATOM list. The atom identifiers need not be unique over all atoms in the CIF; they need only be unique for each atom in a monomer. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_atom.atom_id' entity_mon_atom yes '_atom_site.label_atom_id' atom_site yes '_entity_mon_angle.atom_id_1' entity_mon_angle yes '_entity_mon_angle.atom_id_2' entity_mon_angle yes '_entity_mon_angle.atom_id_3' entity_mon_angle yes '_entity_mon_bond.atom_id_1' entity_mon_bond yes '_entity_mon_bond.atom_id_2' entity_mon_bond yes '_entity_mon_chir.atom_id' entity_mon_chir yes '_entity_mon_chir_atom.atom_id' entity_mon_chir_atom yes '_entity_mon_plane_atom.atom_id' entity_mon_plane_atom yes '_entity_mon_tor.atom_id_1' entity_mon_tor yes '_entity_mon_tor.atom_id_2' entity_mon_tor yes '_entity_mon_tor.atom_id_3' entity_mon_tor yes '_entity_mon_tor.atom_id_4' entity_mon_tor yes '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_angle.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_bond.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_chir.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_chir_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_plane_atom.atom_id' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_1' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_2' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_3' '_entity_mon_atom.atom_id' '_entity_mon_tor.atom_id_4' '_entity_mon_atom.atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code char
_item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_entity_mon_atom.charge' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0 _item_range.maximum 6 _item_range.minimum -6 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion'
save_entity_mon_atom.model_cartn_x.
_item_description.description ; The x component of the coordinates for this atom in this monomer specified as orthogonal Angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site_ list. ; _item.name '_entity_mon_atom.model_cartn_x' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' loop_ _item_dependent.dependent_name '_entity_mon_atom.model_cartn_y' '_entity_mon_atom.model_cartn_z' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_x_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_atom.model_cartn_x. ; _item.name '_entity_mon_atom.model_cartn_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_entity_mon_atom.model_cartn_y_esd' '_entity_mon_atom.model_cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_y.
_item_description.description ; The y component of the coordinates for this atom in this monomer specified as orthogonal Angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site_ list. ; _item.name '_entity_mon_atom.model_cartn_y' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' loop_ _item_dependent.dependent_name '_entity_mon_atom.model_cartn_x' '_entity_mon_atom.model_cartn_z' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_y_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_atom.model_cartn_y. ; _item.name '_entity_mon_atom.model_cartn_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_entity_mon_atom.model_cartn_x_esd' '_entity_mon_atom.model_cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_z.
_item_description.description ; The x component of the coordinates for this atom in this monomer specified as orthogonal Angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site_ list. ; _item.name '_entity_mon_atom.model_cartn_z' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' loop_ _item_dependent.dependent_name '_entity_mon_atom.model_cartn_x' '_entity_mon_atom.model_cartn_y' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_z_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_atom.model_cartn_z. ; _item.name '_entity_mon_atom.model_cartn_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_entity_mon_atom.model_cartn_x_esd' '_entity_mon_atom.model_cartn_y_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_entity_mon_atom.substruct_code.
_item_description.description ; This data item assigns the atom to a substructure of the monomer, if appropriate. ; _item.name '_entity_mon_atom.substruct_code' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail main 'main chain of an amino acid' side 'side chain of an amino acid' base 'base of a nucleic acid' phos 'phosphate of a nucleic acid' sugar 'sugar of a nucleic acid' none 'not appropriate for this monomer'
save_entity_mon_atom.type_symbol.
_item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ;
_category.description ; Data items in the ENTITY_MON_BOND category record details about the bonds between atoms in the monomer entity. Target values may be specified as bond orders, as a distance between the two atoms, or both. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_bond.mon_id' '_entity_mon_bond.atom_id_1' '_entity_mon_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_bond.mon_id _entity_mon_bond.atom_id_1 _entity_mon_bond.atom_id_2 _entity_mon_bond.value_order _entity_mon_bond.value_dist phe N CA sing x.xx phe CA C sing x.xx phe C O doub x.xx phe CB CA sing x.xx phe CB CG sing x.xx phe CG CD1 arom x.xx phe CD1 CE1 arom x.xx phe CE1 CZ arom x.xx phe CZ CE2 arom x.xx phe CE2 CD2 arom x.xx phe CD2 CG arom x.xx val N CA sing x.xx val CA C sing x.xx val C O doub x.xx val CB CA sing x.xx val CB CG1 sing x.xx val CB CG2 sing x.xx ;
save_entity_mon_bond.atom_id_1.
_item_description.description ; The id of the first of the two atoms that define the bond. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ; _item_dependent.dependent_name '_entity_mon_bond.atom_id_2'
save_entity_mon_bond.atom_id_2.
_item_description.description ; The id of the second of the two atoms that define the bond. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ; _item_dependent.dependent_name '_entity_mon_bond.atom_id_1'
_item_description.description ; This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_entity_mon_bond.value_dist.
_item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_entity_mon_bond.value_dist' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_entity_mon_bond.value_dist_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_bond.value_dist. ; _item.name '_entity_mon_bond.value_dist_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_entity_mon_bond.value_order.
_item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_entity_mon_bond.value_order' _item.category_id _item.category_id _item.mandatory_code no _item_default.value sing _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalised double bond' pi 'pi bond'
_category.description ; Data items in the ENTITY_MON_CHIR category provide detail about the chiral centers in a monomer entity. The atoms bonded to the chiral atom are specified in the ENTITY_MON_CHIR_ATOM category. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_chir.mon_id' '_entity_mon_chir.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_chir.mon_id _entity_mon_chir.id _entity_mon_chir.atom_id phe phe1 CA val val1 CA # - - - - data truncated for brevity - - - - ;
_item_description.description ; The id of the atom that is a chiral center. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ;
_item_description.description ; The value of _entity_mon_chir.id must uniquely identify a record in the ENTITY_MON_CHIR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_chir.id' entity_mon_chir yes '_entity_mon_chir_atom.chir_id' entity_mon_chir_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_mon_chir_atom.chir_id' '_entity_mon_chir.id' _item_type.code char
_item_description.description ; This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_entity_mon_chir.number_atoms_all.
_item_description.description ; The total number of atoms bonded to the atom specified by _entity_mon_chir.atom_id. ; _item.name '_entity_mon_chir.number_atoms_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon_chir.number_atoms_nh.
_item_description.description ; The number of non-hydrogen atoms bonded to the atom specified by _entity_mon_chir.atom_id. ; _item.name '_entity_mon_chir.number_atoms_nh' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon_chir.volume_flag.
_item_description.description ; A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. ; _item.name '_entity_mon_chir.volume_flag' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail sign 'match magnitude and sign' nosign 'match magnitude only'
save_entity_mon_chir.volume_three.
_item_description.description ; The chiral volume Vc, for chiral centers that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. Vc = V1 * [ V2 X V3 ] V1, V2 and V3 are vector distances from _entity_mon_chir.atom_id V1 is the distance to the first atom tin the ENTITY_MON_CHIR_ATOM list, V1 the distance to the second, and V3 the distance to the third. * indicates the vector dot product, and X indicate the vector cross product. ; _item.name '_entity_mon_chir.volume_three' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms_cubed'
save_entity_mon_chir.volume_three_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_chir.volume_three. ; _item.name '_entity_mon_chir.volume_three_esd' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'angstroms_cubed'
_category.description ; Data items in the ENTITY_MON_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a monomer entity. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_chir_atom.chir_id' '_entity_mon_chir_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_chir_atom.chir_id _entity_mon_chir_atom.atom_id phe1 N phe1 C phe1 CB val1 N val1 C val1 CB # - - - - data truncated for brevity - - - - ;
save_entity_mon_chir_atom.atom_id.
_item_description.description ; The id of an atom bonded to the chiral atom. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ;
save_entity_mon_chir_atom.chir_id.
_item_description.description ; This data item is a pointer to _entity_mon_chir.id in the ENTITY_MON_CHIR category. ;
save_entity_mon_chir_atom.dev.
_item_description.description ; The estimated standard deviation of the position of this atom from the plane defined by all of the atoms in the plane. ; _item.name '_entity_mon_chir_atom.dev' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'angstroms'
_category.description ; Data items in the ENTITY_MON_PLANE category provide identifiers for the planes in a monomer entity. The atoms in the plane are specified in the ENTITY_MON_PLANE_ATOM category. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_plane.mon_id' '_entity_mon_plane.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_plane.mon_id _entity_mon_plane.id phe phe1 ;
_item_description.description ; The value of _entity_mon_plane.id must uniquely identify a record in the ENTITY_MON_PLANE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_plane.id' entity_mon_plane yes '_entity_mon_plane_atom.plane_id' entity_mon_plane_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_mon_plane_atom.plane_id' '_entity_mon_plane.id' _item_type.code char
_item_description.description ; This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_entity_mon_plane.number_atoms_all.
_item_description.description ; The total number of atoms in the plane. ; _item.name '_entity_mon_plane.number_atoms_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon_plane.number_atoms_nh.
_item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_entity_mon_plane.number_atoms_all_nh' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
_category.description ; Data items in the ENTITY_MON_PLANE_ATOM category enumerate the atoms in a plane within a monomer entity. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_plane_atom.plane_id' '_entity_mon_plane_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_plane_atom.plane_id _entity_mon_plane_atom.atom_id phe1 CB phe1 CG phe1 CD1 phe1 CE1 phe1 CZ phe1 CE2 phe1 CD2 ;
save_entity_mon_plane_atom.atom_id.
_item_description.description ; The id of an atom involved in the plane. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ;
save_entity_mon_plane_atom.plane_id.
_item_description.description ; This data item is a pointer to _entity_mon_plane.id in the ENTITY_MON_PLANE category. ;
_category.description ; Data items in the ENTITY_MON_TOR category record details about the torsion angles in a monomer entity. As torsion angles can have more than one target value, the target values are specified in the ENTITY_MON_TOR_VALUE category. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_mon_tor.mon_id' '_entity_mon_tor.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_tor.mon_id _entity_mon_tor.id _entity_mon_tor.atom_id_1 _entity_mon_tor.atom_id_2 _entity_mon_tor.atom_id_3 _entity_mon_tor.atom_id_4 phe phe_chi1 N CA CB CG phe phe_chi2 CA CB CG CD1 phe phe_ring1 CB CG CD1 CE1 phe phe_ring2 CB CG CD2 CE2 phe phe_ring3 CG CD1 CE1 CZ phe phe_ring4 CD1 CE1 CZ CE2 phe phe_ring5 CE1 CZ CE2 CD2 ;
save_entity_mon_tor.atom_id_1.
_item_description.description ; The id of the first of the four atoms that define the torsion angle. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ; loop_ _item_dependent.dependent_name '_entity_mon_tor.atom_id_2' '_entity_mon_tor.atom_id_3' '_entity_mon_tor.atom_id_4'
save_entity_mon_tor.atom_id_2.
_item_description.description ; The id of the second of the four atoms that define the torsion angle. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ; loop_ _item_dependent.dependent_name '_entity_mon_tor.atom_id_1' '_entity_mon_tor.atom_id_3' '_entity_mon_tor.atom_id_4'
save_entity_mon_tor.atom_id_3.
_item_description.description ; The id of the third of the four atoms that define the torsion angle. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ; loop_ _item_dependent.dependent_name '_entity_mon_tor.atom_id_1' '_entity_mon_tor.atom_id_2' '_entity_mon_tor.atom_id_4'
save_entity_mon_tor.atom_id_4.
_item_description.description ; The id of the fourth of the four atoms that define the torsion angle. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ; loop_ _item_dependent.dependent_name '_entity_mon_tor.atom_id_1' '_entity_mon_tor.atom_id_2' '_entity_mon_tor.atom_id_3'
_item_description.description ; The value of _entity_mon_tor.id must uniquely identify a record in the ENTITY_MON_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_mon_tor.id' entity_mon_tor yes '_entity_mon_tor_value.tor_id' entity_mon_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_mon_tor_value.tor_id' '_entity_mon_tor.id' _item_type.code char
_item_description.description ; This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
_category.description ; Data items in the ENTITY_MON_TOR_VALUE category record details about the target values for the torsion angles enumerated in the ENTITY_MON_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_mon_tor_value.tor_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_mon_tor_value.tor_id _entity_mon_tor_value.angle _entity_mon_tor_value.dist phe_chi1 -60.0 2.88 phe_chi1 180.0 3.72 phe_chi1 60.0 2.88 phe_chi2 90.0 3.34 phe_chi2 -90.0 3.34 phe_ring1 180.0 3.75 phe_ring2 180.0 3.75 phe_ring3 0.0 2.80 phe_ring4 0.0 2.80 phe_ring5 0.0 2.80 ;
save_entity_mon_tor_value.angle.
_item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. ; _item.name '_entity_mon_tor_value.angle' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum 180.0 _item_range.minimum -180.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
save_entity_mon_tor_value.angle_esd.
_item_description.description ; The estimated statard deviation of _entity_mon_tor_value.angle. ; _item.name '_entity_mon_tor_value.angle_esd' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum 180.0 _item_range.minimum -180.0 _item_type.code float _item_units.code 'degrees'
save_entity_mon_tor_value.dist.
_item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _entity_mon_tor.atom_id_1 and _entity_mon_tor.atom_id_4 in the referenced record in the ENTITY_MON_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 will yield the same distance as a 60 degree angle). However the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. ; _item.name '_entity_mon_tor_value.dist' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_entity_mon_tor_value.dist_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_tor_value.dist_esd. ; _item.name '_entity_mon_tor_value.dist_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_entity_mon_tor_value.tor_id.
_item_description.description ; This data item is a pointer to _entity_mon_tor.id in the ENTITY_MON_TOR category. ;
_category.description ; Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some case, the entity name may not be the same as the name of the biological structure. For instance, hemoglobin alpha chain would be the entity common name, not hemoglobin. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_name_com.entity_id' '_entity_name_com.name' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_name_com.entity_id _entity.name_com.name 1 'HIV-1 protease monomer' 1 'HIV-1 PR monomer' 2 'acetyl-pepstatin' 2 'acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine' 3 'water' ;
save_entity_name_com.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; A common name for the entity. ; _item.name '_entity_name_com.name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'HIV protease monomer' 'hemoglobin alpha chain' '2-fluoro-1,4-dichloro benzene'
_category.description ; Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity, and tell which system was is the source of the systematic name. In some case, the entity name may not be the same as the name of the biological structure. For instance, hemoglobin alpha chain would be the entity common name, not hemoglobin. ; _category.id _category.id _category.mandatory_code _category_key.name _category_key.name loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_name_sys.entity_id _entity_name_sys.name 1 ECx.x.x.x 2 'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta' 3 'H(2)0' ;
save_entity_name_sys.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; The systematic name for the entity. ; _item.name '_entity_name_sys.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'x,x,pyranoside' 'EC 2.1.1.1' '2-fluoro-1,4-dichloro benzene'
_item_description.description ; The system used to generate the systematic name of the entity. ; _item.name '_entity_name_sys.system' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'chemical abstracts conventions' 'enzyme convention' 'Sigma catalog'
_category.description ; Data items in the ENTITY_POLY category... ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_poly.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_chirality _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.type_details 1 polypeptide(L) no no no . ;
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
save_entity_poly.nstd_chirality.
_item_description.description ; A flag to indicate whether or not the polymer contains at least one monomer unit with chirality different from that specified in _entity_poly.type. ; _item.name '_entity_poly.nstd_chirality' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value yes no
save_entity_poly.nstd_linkage.
_item_description.description ; A flag to indicate whether or not the polymer contains at least one monomer-to-monomer linkage different from that implied by _entity_poly.type. ; _item.name '_entity_poly.nstd_linkage' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value yes no
save_entity_poly.nstd_monomer.
_item_description.description ; A flag to indicate whether or not the polymer contains at least one monomer that is not considered standard. ; _item.name '_entity_poly.nstd_monomer' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value yes no
save_entity_poly.number_of_monomers.
_item_description.description ; The number of monomers in the polymer. ; _item.name '_entity_poly.number_of_monomers' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
_item_description.description ; The type of the polymer. ; _item.name '_entity_poly.type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value 'polypeptide(D)' 'polypeptide(L)' 'polydeoxyribonucleotide' 'polyribonucleotide' 'polysaccharide(D)' 'polysaccharide(L)' 'other'
save_entity_poly.type_details.
_item_description.description ; A description of special aspects of the polymer type. ; _item.name '_entity_poly.type_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'monomer Ala 16 is a D-amino acid' ; the oligomer contains alternating RNA and DNA units ;
_category.description ; Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer id - the corresponding ATOM_SITE entries should reflect this heterogeneity. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_poly_seq.entity_id' '_entity_poly_seq.num' '_entity_poly_seq.mon_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 PRO 1 2 GLN 1 3 ILE 1 4 THR 1 5 LEU 1 6 TRP 1 7 GLN 1 8 ARG 1 9 PRO 1 10 LEU 1 11 VAL 1 12 THR 1 13 ILE 1 14 LYS 1 15 ILE 1 16 GLY 1 17 GLY 1 18 GLN 1 19 LEU 1 20 LYS 1 21 GLU 1 22 ALA 1 23 LEU 1 24 LEU 1 25 ASP # - - - - data truncated for brevity - - - - ;
save_entity_poly_seq.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; A flag to indicate whether or not this monomer in the polymer is heterogeneous in sequence. This would be a rare phenomenon. ; _item.name '_entity_poly_seq.hetero' _item.category_id _item.category_id _item.mandatory_code no _item_default.value no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail no ; the sequence is not heterogenous at this monomer ; n 'abbreviation for "no"' yes ; the sequence is heterogenous at this monomer ; y 'abbreviation for "yes"'
_item_description.description ; This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
_item_description.description ; The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number, and that the sequence numbers must progress in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_poly_seq.num' entity_poly_seq yes '_atom_site.entity_seq_num' atom_site yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.entity_seq_num' '_entity_poly_seq.num' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
_item_description.description ; The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number, and that the sequence numbers must progress in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_poly_seq.num' entity_poly_seq yes '_atom_site.entity_seq_num' atom_site yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.entity_seq_num' '_entity_poly_seq.num' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
_category.description ; Data items in the ENTITY_POLY_SEQ_DIF category provide a mechanism for indicating and annotating differences between the sequence of the entity reported in the data block and a sequence referenced in the ENTITY_REFERENCE data items. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_entity_poly_seq_dif.entity_id' '_entity_poly_seq_dif.seq_num' '_entity_poly_seq_dif.mon_id' '_entity_poly_seq_dif.db_code' '_entity_poly_seq_dif.db_name' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
save_entity_poly_seq_dif.db_mon_id.
_item_description.description ; The monomer type found at this position in the database entry indicated by _entity_mon_seq_dif.db_code and _entity_mon_sequ_dif.db_name. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_entity_poly_seq_dif.details.
_item_description.description ; A description of special aspects of the difference between the sequence reported in the database and the sequence reported in this data block. ; _item.name '_entity_poly_seq_dif.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'strain difference' 'potential sequencing error'
save_entity_poly_seq_dif.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
save_entity_poly_seq_dif.mon_id.
_item_description.description ; The monomer type found at this position in the entity described in this data block. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_entity_poly_seq_dif.seq_num.
_item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ;
_category.description ; Data items in the ENTITY_REFERENCE category... ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_reference.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - example is completely hypothetical ; ; loop_ _entity_reference.entity_id _entity_reference.database_name _entity_reference.database_code _entity_reference.details 1 'Genbank' '12345' ; The strain of HIV-1 protease used in this study contains Asn at position 37. The Genbank sequence cited here has Ser at that position. ; 2 'PDB' '1ABC' ; The structure of the closely related compound, isobutyryl-pepstatin (pepstatin A) in complex with rizopuspepsin ; ;
save_entity_reference.database_code.
_item_description.description ; The code for this entity or a closely related entity in the named database. If this is a sequence database and there are difference between the database sequence and the structure reported in this data block, those difference may be indicated and annotated using the ENTITY_POLY_SEQ_DIF data items. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_reference.database_code' entity_reference yes '_entity_poly_seq_dif.db_code' entity_poly_seq_dif yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_poly_seq_dif.db_code' '_entity_reference.database_code' _item_type.code char loop_ _item_examples.case '1ABC' 'ABCDEF'
save_entity_reference.database_code.
_item_description.description ; The code for this entity or a closely related entity in the named database. If this is a sequence database and there are difference between the database sequence and the structure reported in this data block, those difference may be indicated and annotated using the ENTITY_POLY_SEQ_DIF data items. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_reference.database_code' entity_reference yes '_entity_poly_seq_dif.db_code' entity_poly_seq_dif yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_poly_seq_dif.db_code' '_entity_reference.database_code' _item_type.code char loop_ _item_examples.case '1ABC' 'ABCDEF'
save_entity_reference.database_name.
_item_description.description ; The name of the database containing reference information about this entity. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_reference.database_name' entity_reference yes '_entity_poly_seq_dif.db_name' entity_poly_seq_dif yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_poly_seq_dif.db_name' '_entity_reference.database_name' _item_type.code char loop_ _item_examples.case 'PDB' 'CSD' 'Genbank'
save_entity_reference.database_name.
_item_description.description ; The name of the database containing reference information about this entity. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_reference.database_name' entity_reference yes '_entity_poly_seq_dif.db_name' entity_poly_seq_dif yes loop_ _item_linked.child_name _item_linked.parent_name '_entity_poly_seq_dif.db_name' '_entity_reference.database_name' _item_type.code char loop_ _item_examples.case 'PDB' 'CSD' 'Genbank'
save_entity_reference.details.
_item_description.description ; A description of special aspects of the relationship between the entity as observed in this structure and the entity as it appears in the named database. ; _item.name '_entity_reference.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_entity_reference.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_category.description ; Data items in the ENTITY_SRC_GEN category records details of the source from which the entity was obtained, in those cases where the source was a genetically manipulated one. The following are treated separately: Items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producting organism (plasmid). ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_src_gen.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_src_gen.entity_id _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.host_org_common_name _entity_src_gen.host_org_genus _entity_src_gen.host_org_species _entity_src_gen.plasmid_name 1 'HIV-1' '?' '?' 'NY-5' 'bacteria' 'Escherichia' 'coli' 'pB322' ;
save_entity_src_gen.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
save_entity_src_gen.gene_src_common_name.
_item_description.description ; The common name of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_common_name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'man' 'yeast' 'bacteria'
save_entity_src_gen.gene_src_details.
_item_description.description ; A description of special aspects of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_entity_src_gen.gene_src_genus.
_item_description.description ; The genus of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_genus' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Homo' 'Saccharomyces' 'Escherichia'
save_entity_src_gen.gene_src_species.
_item_description.description ; The species of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_species' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'sapiens' 'cerevisiae' 'coli'
save_entity_src_gen.gene_src_strain.
_item_description.description ; The strain of the natural organism from which the gene was obtained, if relevant. ; _item.name '_entity_src_gen.gene_src_strain' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'DH5a' 'BMH 71-18'
save_entity_src_gen.gene_src_tissue.
_item_description.description ; The tissue of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_tissue' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'heart' 'liver' 'eye lens'
save_entity_src_gen.gene_src_tissue_fraction.
_item_description.description ; The sub-cellular fraction of the tissue of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_tissue_fraction' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'mitochondria' 'nucleus' 'membrane'
save_entity_src_gen.host_org_common_name.
_item_description.description ; The common name of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_common_name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'yeast' 'bacteria'
save_entity_src_gen.host_org_details.
_item_description.description ; A description of special aspects of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_entity_src_gen.host_org_genus.
_item_description.description ; The genus of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_genus' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Saccharomyces' 'Escherichia'
save_entity_src_gen.host_org_species.
_item_description.description ; The species of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_species' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'cerevisiae' 'coli'
save_entity_src_gen.host_org_strain.
_item_description.description ; The strain of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_strain' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'DH5a' 'BMH 71-18'
save_entity_src_gen.plasmid_details.
_item_description.description ; A description of special aspects of the plasmid that produced the entity in the host organism. ; _item.name '_entity_src_gen.plasmid_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_entity_src_gen.plasmid_name.
_item_description.description ; The name of the plasmid that produced the entity in the host organism. ; _item.name '_entity_src_gen.plasmid_name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'pET3C' 'pT123sab'
_category.description ; Data items in the ENTITY_SRC_NAT category records details of the source from which the entity was obtained, in those cases where the entity was isolated directly from a natural tissue. ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_src_nat.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_src_nat.entity_id _entity_src_nat.common_name _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.details 2 'bacteria' 'Actinomycetes' '?' ; Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture University, and provided to us by Dr. Ben Dunn, University of Florida, and Dr. J. Kay, University of Wales. ; ;
save_entity_src_nat.common_name.
_item_description.description ; The genus of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.common_name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'man' 'yeast' 'bacteria'
_item_description.description ; A description of special aspects of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_entity_src_nat.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; The genus of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.genus' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Homo' 'Saccharomyces' 'Escherichia'
_item_description.description ; The species of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.species' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'sapiens' 'cerevisiae' 'coli'
_item_description.description ; The strain of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.strain' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'DH5a' 'BMH 71-18'
_item_description.description ; The tissue of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.tissue' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'heart' 'liver' 'eye lens'
save_entity_src_nat.tissue_fraction.
_item_description.description ; The sub-cellular fraction of the tissue of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.tissue_fraction' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'mitochondria' 'nucleus' 'membrane'
_category.description ; Data items in the EXPTL category record details about the growth of the crystal, and about experimental measurements on the crystal, such as shape, size, density, and so on. ; _category.id _category.id _category.mandatory_code no _category_key.name '_exptl.block_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _exptl.absorpt_coefficient_mu 0.59 _exptl.absorpt_correction_type 'shelx76 gaussian' _exptl.absorpt_correction_T_min .933 _exptl.absorpt_correction_T_max .824 ;
save_exptl.absorpt_coefficient_mu.
_item_description.description ; The absorption coefficient mu calculated from atomic content of the cell, the density and the radiation wavelength. ; _item.name '_exptl.absorpt_coefficient_mu' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_coefficient_mu' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'reciprocal_millimetres'
save_exptl.absorpt_correction_T_max.
_item_description.description ; The maximum transmission factors for the crystal and radiation. These factors are also referred to as the absorption correction A or 1/A*. ; _item.name '_exptl.absorpt_correction_T_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_T_max' _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
save_exptl.absorpt_correction_T_min.
_item_description.description ; The minimum transmission factors for the crystal and radiation. These factors are also referred to as the absorption correction A or 1/A*. ; _item.name '_exptl.absorpt_correction_T_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_T_min' _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
save_exptl.absorpt_correction_type.
_item_description.description ; The absorption correction type and method. ; _item.name '_exptl.absorpt_correction_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_type' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail analytical 'analytical from crystal shape' integration 'integration from crystal shape' empirical 'empirical from diffraction data' refdelf 'refined from delta-F' sphere 'spherical' cylinder 'cylindrical' none 'no absorption correction applied'
save_exptl.absorpt_process_details.
_item_description.description ; Description of the absorption process applied to the data. ; _item.name '_exptl.absorpt_process_details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_process_details' _item_type.code char _item_examples.case 'Tompa analytical'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The total number of crystals used in the data measurement. ; _item.name '_exptl.crystals_number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystals_number' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
_item_description.description ; Any special information about the experimental work prior to the diffraction measurement. See also _exptl.crystal_preparation. ; _item.name '_exptl.details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_special_details' _item_type.code char
_category.description ; Data items in the EXPTL_CRYSTAL category record details about experimental measurements on the crystal or crystals used, such as shape, size, density, and so on. ; _category.id _category.id _category.mandatory_code no _category_key.name '_exptl_crystal.id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _exptl_crystal.description prism _exptl_crystal.colour colourless _exptl_crystal.size_max 0.32 _exptl_crystal.size_mid 0.27 _exptl_crystal.size_min 0.10 _exptl_crystal.density_diffrn 1.146 _exptl_crystal.density_meas ? _exptl_crystal.F_000 656 ;
_item_description.description ; The colour of the crystal. ; _item.name '_exptl_crystal.colour' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_colour' _item_type.code char _item_examples.case 'Dark green'
save_exptl_crystal.density_diffrn.
_item_description.description ; Density values calculated from crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). ; _item.name '_exptl_crystal.density_diffrn' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_diffrn' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_exptl_crystal.density_meas.
_item_description.description ; Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). ; _item.name '_exptl_crystal.density_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_meas' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_exptl_crystal.density_meas_temp.
_item_description.description ; Temperature in degrees Kelvin at which _exptl_crystal.density_meas was determined. ; _item.name '_exptl_crystal.density_meas_temp' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_meas_temp' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'kelvin'
save_exptl_crystal.density_method.
_item_description.description ; The method used to measure _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_method' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_method' _item_type.code char
save_exptl_crystal.density_percent_sol.
_item_description.description ; Density value calculated from crystal cell and contents, expressed as percent solvent. P = 1 - (1.23 * N * Mmass) / V where N is the number of molecules in the unit cell Mmass is the molecular mass of each molecule (gm/mole) V is the volume of the unit cell (A^3) and 1.23 is the product of: (0.74 cm^3/gm^3) * (10^24 A^3/cm^3) / (6.02*10^23) moles/molecule where 0.74 is an assumed value for the partial specific volume of the molecule ; _item.name '_exptl_crystal.density_percent_sol' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_exptl_crystal.description.
_item_description.description ; A description of the crystal quality and habit. Dimensional data is better placed in the _exptl_crystal.face_ data items. ; _item.name '_exptl_crystal.description' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_description' _item_type.code char
_item_description.description ; The effective number of electrons in the crystal unit cell contributing to F(000). It may contain dispersion contributions. ; _item.name '_exptl_crystal.F_000' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_F_000' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
_item_description.description ; The value of _exptl_crystal.id must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_exptl_crystal.id' exptl_crystal yes '_exptl_crystal_grow.crystal_id' exptl_crystal yes '_diffrn_refln.crystal_id' diffrn_refln yes '_refln.crystal_id' refln yes _item_aliases.alias_name '_exptl_crystal_id' loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.crystal_id' '_exptl_crystal.id' '_exptl_crystal_grow.crystal_id' '_exptl_crystal.id' '_refln.crystal_id' '_exptl_crystal.id' _item_type.code char
_item_description.description ; The value of _exptl_crystal.id must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_exptl_crystal.id' exptl_crystal yes '_exptl_crystal_grow.crystal_id' exptl_crystal yes '_diffrn_refln.crystal_id' diffrn_refln yes '_refln.crystal_id' refln yes _item_aliases.alias_name '_exptl_crystal_id' loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.crystal_id' '_exptl_crystal.id' '_exptl_crystal_grow.crystal_id' '_exptl_crystal.id' '_refln.crystal_id' '_exptl_crystal.id' _item_type.code char
save_exptl_crystal.preparation.
_item_description.description ; Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the diffraction measurements. ; _item.name '_exptl_crystal.preparation' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_preparation' _item_type.code char _item_examples.case 'mounted in an argon-filled quartz capillary'
_item_description.description ; The maximum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals used in the experiment. ; _item.name '_exptl_crystal.size_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_max' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'millimetres'
_item_description.description ; The medial dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals used in the experiment. ; _item.name '_exptl_crystal.size_mid' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_mid' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'millimetres'
_item_description.description ; The minimum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals used in the experiment. ; _item.name '_exptl_crystal.size_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_min' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'millimetres'
_item_description.description ; The radius of the crystal, If the crystal is a sphere or a cylinder. This item may appear in a list with _exptl_crystal.id if multiple crystals used in the experiment. ; _item.name '_exptl_crystal.size_rad' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_rad' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'millimetres'
_category.description ; Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_k' '_exptl_crystal_face.index_l' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ; ; Example 2 - based on ; ; Need Example 2 ;
save_exptl_crystal_face.diffr_chi.
_item_description.description ; The chi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_chi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_chi' _item_type.code float _item_units.code 'degrees'
save_exptl_crystal_face.diffr_kappa.
_item_description.description ; The kappa diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_kappa' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_kappa' _item_type.code float _item_units.code 'degrees'
save_exptl_crystal_face.diffr_phi.
_item_description.description ; The phi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_phi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_phi' _item_type.code float _item_units.code 'degrees'
save_exptl_crystal_face.diffr_psi.
_item_description.description ; The psi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_psi' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_psi' _item_type.code float _item_units.code 'degrees'
save_exptl_crystal_face.index_h.
_item_description.description ; Miller index h of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_exptl_crystal_face_index_h' loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_k' '_exptl_crystal_face.index_l' _item_type.code int
save_exptl_crystal_face.index_k.
_item_description.description ; Miller index k of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_exptl_crystal_face_index_k' loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_l' _item_type.code int
save_exptl_crystal_face.index_l.
_item_description.description ; Miller index l of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_exptl_crystal_face_index_l' loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_k' _item_type.code int
save_exptl_crystal_face.perp_dist.
_item_description.description ; The perpendicular distance of the face to centre of rotation of the crystal. ; _item.name '_exptl_crystal_face.perp_dist' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_perp_dist' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'millimetres'
_category.description ; Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal. ; _category.id _category.id _category.mandatory_code no _category_key.name '_exptl_crystal_grow.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'hanging drop' _exptl_crystal_grow.apparatus 'Linbro plates' _exptl_crystal_grow.atmosphere 'room air' _exptl_crystal_grow.pH 4.7 _exptl_crystal_grow.temp 18(3) _exptl_crystal_grow.time 'approximately 2 days' ;
save_exptl_crystal_grow.apparatus.
_item_description.description ; The physical apparatus in which the crystal was grown. ; _item.name '_exptl_crystal_grow.apparatus' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Linbro plate' 'sandwich box' 'ACA plates'
save_exptl_crystal_grow.atmosphere.
_item_description.description ; The nature of the gas or gas mixture in which the crystal was grown. ; _item.name '_exptl_crystal_grow.atmosphere' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'room air' 'nitrogen' 'argon'
save_exptl_crystal_grow.crystal_id.
_item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ;
save_exptl_crystal_grow.details.
_item_description.description ; A description of special aspects of the crystal growth. ; _item.name '_exptl_crystal_grow.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. ; ; Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. ; ; The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. ;
save_exptl_crystal_grow.method.
_item_description.description ; The method used to grow the crystals. ; _item.name '_exptl_crystal_grow.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'batch precipitation' 'batch dialysis' 'hanging drop vapor diffusion' 'sitting drop vapor diffusion'
save_exptl_crystal_grow.method_ref.
_item_description.description ; A literature reference that describes the method used to grow the crystals. ; _item.name '_exptl_crystal_grow.method_ref' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'McPherson et al., 1988'
_item_description.description ; The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in _exptl_crystal_grow.details. ; _item.name '_exptl_crystal_grow.pH' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float loop_ _item_examples.case 7.4 7.6 4.3
save_exptl_crystal_grow.pressure.
_item_description.description ; The ambient pressure in kilopascals at which the crystal was grown. ; _item.name '_exptl_crystal_grow.pressure' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'kilopascals'
save_exptl_crystal_grow.pressure_esd.
_item_description.description ; The estimated standard deviation of _exptl_crystal_grow.pressure. ; _item.name '_exptl_crystal_grow.pressure_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kilopascals'
save_exptl_crystal_grow.seeding.
_item_description.description ; A description of the protocol used for seeding the crystal growth. ; _item.name '_exptl_crystal_grow.seeding' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'macroseeding' ; Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. ;
save_exptl_crystal_grow.seeding_ref.
_item_description.description ; A literature reference that describes the protocol used to seed the crystal. ; _item.name '_exptl_crystal_grow.seeding_ref' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'Stura et al., 19xx'
_item_description.description ; The temperature in degress Kelvin at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in _exptl_crystal_grow.details. ; _item.name '_exptl_crystal_grow.temp' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'kelvin'
save_exptl_crystal_grow.temp_esd.
_item_description.description ; The estimated standard deviation of _exptl_crystal_grow.temp. ; _item.name '_exptl_crystal_grow.temp_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kelvin'
_item_description.description ; The approximate time that the crystal took to grow to the size used for data collection. ; _item.name '_exptl_crystal_grow.time' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'overnight' '2-4 days' '6 months'
_category.description ; Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 will be the solution that contains the molecule to be crystallized and solution 2 will be the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be described in EXPTL_CRYSTAL_GROW_DETAILS, using the solutions described in EXPTL_CRYSTAL_GROW_COMP. ; _category.id _category.id _category.mandatory_code no _category_key.name '_exptl_crystal_grow_comp.id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 'HIV-1 protease' '0.002 ml' '6 mg/ml' ; The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide ; 2 2 'NaCl' '0.200 ml' '4 M' 'in 3 mM NaAzide' 3 2 'Acetic Acid' '0.047 ml' '100 mM' 'in 3 mM NaAzide' 4 2 'Na Acetate' '0.053 ml' '100 mM' ; in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. ; 5 2 'water' '0.700 ml' 'neat' 'in 3 mM NaAzide' ;
save_exptl_crystal_grow_comp.conc.
_item_description.description ; The concentration of the solution component. ; _item.name '_exptl_crystal_grow_comp.conc' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '200 \ml' '0.1 ml'
save_exptl_crystal_grow_comp.details.
_item_description.description ; A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. ; _item.name '_exptl_crystal_grow_comp.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'in 3 mM NaAzide' ; The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide ; ; in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. ;
save_exptl_crystal_grow_comp.id.
_item_description.description ; The value of _exptl_crystal_grow_comp.id must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_exptl_crystal_grow_comp.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 1 A 'protein in buffer'
save_exptl_crystal_grow_comp.name.
_item_description.description ; A common name for the component of the solution. ; _item.name '_exptl_crystal_grow_comp.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'protein in buffer' 'acetic acid'
save_exptl_crystal_grow_comp.sol_id.
_item_description.description ; An identifier for the solution to which the given solution component belongs. ; _item.name '_exptl_crystal_grow_comp.sol_id' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 1 'well solution' 'solution A'
save_exptl_crystal_grow_comp.volume.
_item_description.description ; The volume of the solution component. ; _item.name '_exptl_crystal_grow_comp.volume' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '200 \ml' '0.1 ml'
_category.description ; Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT and GEOM_TORSION) categories record details about the molecular and crystal geometry, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the CIF. They serve, however, the dual purpose of providing a check on the correctness of both sets of data, and of enabling the most important geometric data to be identified for publication by setting the appropriate publication flag. ; _category.id _category.id _category.mandatory_code no _category_key.name '_geom.block_id' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The description of geometrical information not covered by the existing GEOM data names, such as least-squares planes. ; _item.name '_geom.details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_special_details' _item_type.code char
_category.description ; Data items in the GEOM_ANGLE category record details about the molecular and crystal angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_geom_angle.atom_site_label_1' '_geom_angle.atom_site_label_2' '_geom_angle.atom_site_label_3' '_geom_angle.site_symmetry_1' '_geom_angle.site_symmetry_2' '_geom_angle.site_symmetry_3' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _geom_angle.atom_site_label_1 _geom_angle.atom_site_label_2 _geom_angle.atom_site_label_3 _geom_angle.value _geom_angle.site_symmetry_1 _geom_angle.site_symmetry_2 _geom_angle.site_symmetry_3 _geom_angle.publ_flag C2 O1 C5 111.6(2) 1_555 1_555 1_555 yes O1 C2 C3 110.9(2) 1_555 1_555 1_555 yes O1 C2 O21 122.2(3) 1_555 1_555 1_555 yes C3 C2 O21 127.0(3) 1_555 1_555 1_555 yes C2 C3 N4 101.3(2) 1_555 1_555 1_555 yes C2 C3 C31 111.3(2) 1_555 1_555 1_555 yes C2 C3 H3 107(1) 1_555 1_555 1_555 ? N4 C3 C31 116.7(2) 1_555 1_555 1_555 yes # - - - - data truncated for brevity - - - - ;
save_geom_angle.atom_site_label_1.
_item_description.description ; The label of the first of the three atom sites that define the angle specified by _geom_angle. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_angle_atom_site_label_1' loop_ _item_dependent.dependent_name '_geom_angle.atom_site_label_2' '_geom_angle.atom_site_label_3'
save_geom_angle.atom_site_label_2.
_item_description.description ; The label of the second of the three atom sites that define the angle specified by _geom_angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_angle_atom_site_label_2' loop_ _item_dependent.dependent_name '_geom_angle.atom_site_label_1' '_geom_angle.atom_site_label_3'
save_geom_angle.atom_site_label_3.
_item_description.description ; The label of the third of the three atom sites that define the angle specified by _geom_angle. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_angle_atom_site_label_3' loop_ _item_dependent.dependent_name '_geom_angle.atom_site_label_1' '_geom_angle.atom_site_label_2'
_item_description.description ; This code signals if the angle is referred to in a publication or should be placed in a table of significant angles. ; _item.name '_geom_angle.publ_flag' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_angle_publ_flag' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"'
save_geom_angle.site_symmetry_1.
_item_description.description ; The symmetry code of the first of the three atom sites that define the angle specified by _geom_angle. ; _item.name '_geom_angle.site_symmetry_1' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_angle_site_symmetry_1' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_geom_angle.site_symmetry_2.
_item_description.description ; The symmetry code of the second of the three atom sites that define the angle specified by _geom_angle. ; _item.name '_geom_angle.site_symmetry_2' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_angle_site_symmetry_2' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_geom_angle.site_symmetry_3.
_item_description.description ; The symmetry code of the third of the three atom sites that define the angle specified by _geom_angle. ; _item.name '_geom_angle.site_symmetry_3' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_angle_site_symmetry_3' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
_item_description.description ; Angle in degrees bounded by the _geom_angle.atom_site_label_1, _geom_angle.atom_site_label__2 and _geom_angle.atom_site_label__3. ; _item.name '_geom_angle.value' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_angle' _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _geom_angle.value. ; _item.name '_geom_angle.value_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees'
_category.description ; Data items in the GEOM_BOND category record details about molecular and crystal bonds, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_geom_bond.atom_site_label_1' '_geom_bond.atom_site_label_2' '_geom_bond.site_symmetry_1' '_geom_bond.site_symmetry_2' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _geom_bond.atom_site_label_1 _geom_bond.atom_site_label_2 _geom_bond.distance _geom_bond.site_symmetry_1 _geom_bond.site_symmetry_2 _geom_bond.publ_flag O1 C2 1.342(4) 1_555 1_555 yes O1 C5 1.439(3) 1_555 1_555 yes C2 C3 1.512(4) 1_555 1_555 yes C2 O21 1.199(4) 1_555 1_555 yes C3 N4 1.465(3) 1_555 1_555 yes C3 C31 1.537(4) 1_555 1_555 yes C3 H3 1.00(3) 1_555 1_555 ? N4 C5 1.472(3) 1_555 1_555 yes # - - - - data truncated for brevity - - - - ;
save_geom_bond.atom_site_label_1.
_item_description.description ; The label of the first of the two atom sites that define the bond specified by _geom_bond.distance. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_bond_atom_site_label_1' _item_dependent.dependent_name '_geom_bond.atom_site_label_2'
save_geom_bond.atom_site_label_2.
_item_description.description ; The label of the second of the two atom sites that define the bond specified by _geom_bond.distance. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_bond_atom_site_label_2' _item_dependent.dependent_name '_geom_bond.atom_site_label_1'
_item_description.description ; The intramolecular bond distance. ; _item.name '_geom_bond.distance' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_bond_distance' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _geom_bond.distance. ; _item.name '_geom_bond.distance_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Signals if the bond distance is referred to in a publication or should be placed in a list of special bond distances. ; _item.name '_geom_bond.publ_flag' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_bond_publ_flag' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail no 'do not include bond in special list' n 'abbreviation for "no"' yes 'do include bond in special list' y 'abbreviation for "yes"'
save_geom_bond.site_symmetry_1.
_item_description.description ; The symmetry code of the first of the two atom sites that define the bond specified by _geom_bond.distance. ; _item.name '_geom_bond.site_symmetry_1' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_bond_site_symmetry_1' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_geom_bond.site_symmetry_2.
_item_description.description ; The symmetry code of the second of the two atom sites that define the bond specified by _geom_bond.distance. ; _item.name '_geom_bond.site_symmetry_2' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_bond_site_symmetry_2' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
_category.description ; Data items in the GEOM_CONTACT category record details about molecular and crystal contacts, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_geom_contact.atom_site_label_1' '_geom_contact.atom_site_label_2' '_geom_contact.site_symmetry_1' '_geom_contact.site_symmetry_2' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne (1991). Acta Cryst. C48, 2262-2264]. ; ; loop_ _geom_contact.atom_site_label_1 _geom_contact.atom_site_label_2 _geom_contact.distance _geom_contact.site_symmetry_1 _geom_contact.site_symmetry_2 _geom_contact.publ_flag O(1) O(2) 2.735(3) . . yes H(O1) O(2) 1.82 . . no ;
save_geom_contact.atom_site_label_1.
_item_description.description ; The label of the first of the two atom sites that define the contact specified by _geom_contact.distance. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_contact_atom_site_label_1' _item_dependent.dependent_name '_geom_contact.atom_site_label_2'
save_geom_contact.atom_site_label_2.
_item_description.description ; The label of the second of the two atom sites that define the contact specified by _geom_contact.distance. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_contact_atom_site_label_2' _item_dependent.dependent_name '_geom_contact.atom_site_label_1'
_item_description.description ; The estimated standard deviation of _geom_contact.distance. ; _item.name '_geom_contact.distance' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Signals if the contact distance is referred to in a publication or should be placed in a list of special contact distances. ; _item.name '_geom_contact.publ_flag' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_contact_publ_flag' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail no 'do not include distance in special list' n 'abbreviation for "no"' yes 'do include distance in special list' y 'abbreviation for "yes"'
save_geom_contact.site_symmetry_1.
_item_description.description ; The symmetry code of the first of the two atom sites that define the contact specified by _geom_contact.distance. ; _item.name '_geom_contact.site_symmetry_1' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_contact_site_symmetry_1' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_geom_contact.site_symmetry_2.
_item_description.description ; The symmetry code of the second of the two atom sites that define the contact specified by _geom_contact.distance. ; _item.name '_geom_contact.site_symmetry_2' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_contact_site_symmetry_2' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
_category.description ; Data items in the GEOM_TORSION category record details about molecular and crystal torsion angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. The torsion angle definition should be that of Klyne, W. and Prelog, V. (1960). Endeavour, 16, 521-528. The vector direction _geom_torsion.atom_site_label_2 to _geom_torsion.atom_site_label_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector site2-site1 onto the projection of the vector site3-site4. Clockwise torsions are positive, anticlockwise torsions are negative. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_geom_torsion.atom_site_label_1' '_geom_torsion.atom_site_label_2' '_geom_torsion.atom_site_label_3' '_geom_torsion.atom_site_label_4' '_geom_torsion.site_symmetry_1' '_geom_torsion.site_symmetry_2' '_geom_torsion.site_symmetry_3' '_geom_torsion.site_symmetry_4' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [(1991). Acta Cryst. C48, 2262-2264]. ; ; loop_ _geom_torsion.atom_site_label_1 _geom_torsion.atom_site_label_2 _geom_torsion.atom_site_label_3 _geom_torsion.atom_site_label_4 _geom_torsion _geom_torsion.site_symmetry_1 _geom_torsion.site_symmetry_2 _geom_torsion.site_symmetry_3 _geom_torsion.site_symmetry_4 _geom_torsion.publ_flag C(9) O(2) C(7) C(2) 71.8(2) . . . . yes C(7) O(2) C(9) C(10) -168.0(3) . . . 2_666 yes C(10) O(3) C(8) C(6) -167.7(3) . . . . yes C(8) O(3) C(10) C(9) -69.7(2) . . . 2_666 yes O(1) C(1) C(2) C(3) -179.5(4) . . . . no O(1) C(1) C(2) C(7) -0.6(1) . . . . no ;
save_geom_torsion.atom_site_label_1.
_item_description.description ; The label of the first of the four atom sites that define the torsion angle specified by _geom_torsion. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_torsion_atom_site_label_1' loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_label_2' '_geom_torsion.atom_site_label_3' '_geom_torsion.atom_site_label_4'
save_geom_torsion.atom_site_label_2.
_item_description.description ; The label of the second of the four atom sites that define the torsion angle specified by _geom_torsion. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_torsion_atom_site_label_2' loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_label_1' '_geom_torsion.atom_site_label_3' '_geom_torsion.atom_site_label_4'
save_geom_torsion.atom_site_label_3.
_item_description.description ; The label of the third of the four atom sites that define the torsion angle specified by _geom_torsion. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_torsion_atom_site_label_3' loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_label_1' '_geom_torsion.atom_site_label_2' '_geom_torsion.atom_site_label_4'
save_geom_torsion.atom_site_label_4.
_item_description.description ; The label of the fourth of the four atom sites that define the torsion angle specified by _geom_torsion. This data item is a pointer to _atom_site.label in the ATOM_SITE category. ; _item_aliases.alias_name '_geom_torsion_atom_site_label_4' loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_label_1' '_geom_torsion.atom_site_label_2' '_geom_torsion.atom_site_label_3'
_item_description.description ; This code signals if the angle is referred to in a publication or should be placed in a table of significant angles. ; _item.name '_geom_torsion.publ_flag' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_torsion_publ_flag' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"'
save_geom_torsion.site_symmetry_1.
_item_description.description ; The symmetry code of the first of the four atom sites that define the torsion angle specified by _geom_torsion. ; _item.name '_geom_torsion.site_symmetry_1' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_torsion_site_symmetry_1' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_geom_torsion.site_symmetry_2.
_item_description.description ; The symmetry code of the second of the four atom sites that define the torsion angle specified by _geom_torsion. ; _item.name '_geom_torsion.site_symmetry_2' _item.category_id _item.category_id _item_aliases.alias_name '_geom_torsion_site_symmetry_2' _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_geom_torsion.site_symmetry_3.
_item_description.description ; The symmetry code of the third of the four atom sites that define the torsion specified by _geom_torsion. ; _item.name '_geom_torsion.site_symmetry_3' _item.category_id _item.category_id _item_aliases.alias_name '_geom_torsion_site_symmetry_3' _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_geom_torsion.site_symmetry_4.
_item_description.description ; The symmetry code of the fourth of the four atom sites that define the torsion angle specified by _geom_torsion. ; _item.name '_geom_torsion.site_symmetry_4' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_torsion_site_symmetry_4' _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
_item_description.description ; The value of the torsion angle in degrees. ; _item.name '_geom_torsion.value' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_torsion' _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _geom_torsion.value. ; _item.name '_geom_torsion.value_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees'
_category.description ; Data items in the JOURNAL category record details about the book keeping entries used by the journal's staff when processing a CIF submitted for publication. Normally the creator of a CIF will not specify these data. The data names are not defined in the dictionary because they are for journal use only. ; _category.id _category.id _category.mandatory_code no _category_key.name '_journal.block_id' loop_ _category_group.id 'inclusive_group' 'journal_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ; ; Example 2 - based on Acta Cryst. file for entry HL0007 of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _journal.date_recd_electronic 91-04-15 _journal.date_from_coeditor 91-04-18 _journal.date_accepted 91-04-18 _journal.date_printers_first 91-08-07 _journal.date_proofs_out 91-08-07 _journal.coeditor_code HL0007 _journal.techeditor_code C910963 _journal.coden_ASTM ACSCEE _journal.name_full 'Acta Crystallographica, Section C' _journal.year 1991 _journal.volume 47 _journal.issue NOV91 _journal.page_first 2276 _journal.page_last 2277 ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_ASTM' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coden_ASTM' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_Cambridge' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coden_Cambridge' _item_type.code char
save_journal.coeditor_address.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_address' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_address' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_code' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_code' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_email' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_email' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_fax' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_fax' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_name' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_name' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_notes' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_notes' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_phone' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_phone' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_accepted' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_accepted' _item_type.code char
save_journal.date_from_coeditor.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_from_coeditor' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_from_coeditor' _item_type.code char
save_journal.date_printers_final.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_final' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_final' _item_type.code char
save_journal.date_printers_first.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_first' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_first' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_in' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_in' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_out' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_out' _item_type.code char
save_journal.date_recd_copyright.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_copyright' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_copyright' _item_type.code char
save_journal.date_recd_electronic.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_electronic' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_electronic' _item_type.code char
save_journal.date_recd_hard_copy.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_hard_copy' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_hard_copy' _item_type.code char
save_journal.date_to_coeditor.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_to_coeditor' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_to_coeditor' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.issue' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_issue' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.name_full' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_name_full' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_first' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_page_first' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_last' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_page_last' _item_type.code char
save_journal.suppl_publ_number.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_number' _item_type.code char
save_journal.suppl_publ_pages.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_pages' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_pages' _item_type.code char
save_journal.techeditor_address.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_address' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_address' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_code' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_code' _item_type.code char
save_journal.techeditor_email.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_email' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_email' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_fax' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_fax' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_name' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_name' _item_type.code char
save_journal.techeditor_notes.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_notes' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_notes' _item_type.code char
save_journal.techeditor_phone.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_phone' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_phone' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.volume' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_volume' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.year' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_year' _item_type.code char
_category.description ; Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. The details about application of each method are listed in the appropriate subcategories. ; _category.id _category.id _category.mandatory_code no _category_key.name '_phasing.method' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - example is completely hypothetical ; ; loop_ _phasing.method 'MIR' 'averaging' ;
_item_description.description ; A listing of the method or methods applied to phase this structure. ; _item.name '_phasing.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail 'averaging' ; phase improvement by averaging over multiple images of the structure ; 'isomorphous' ; phasing begining with phases calculated from a isomorphous structure ; 'MAD' ; phasing by multiple-wavelength anomalous dispersion ; 'MIR' ; phasing by multiple isomorphous replacement ; 'MR' ; phasing by molecular replacement ;
_category.description ; Data items in the PHASING_AVERAGING category record details about the phasing of the structure, when methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved. ; _category.id _category.id _category.mandatory_code no _category_key.name '_phasing_averaging.block_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - example is completely hypothetical ; ; _phasing_averaging.method ; Iterative 3-fold averaging alternating with phase extensions by 0.5 reciprocal lattice units per cycle according to the method described by X and Y (ref). ; _phasing_averaging.details ; The position of the 3-fold axis was redetermined every five cycles. ; ;
save_phasing_averaging.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_phasing_averaging.details.
_item_description.description ; A description of special aspects of the averaging process. ; _item.name '_phasing_averaging.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Position of the 3-fold axis was redetermined every five cycles. ;
save_phasing_averaging.method.
_item_description.description ; A description of the phase averaging phasing method applied to phase this structure. Note that this is not the computer program used, which is described in _computing.phasing_averaging. Rather this data item should be used to describe significant methodological options used within the phase averaging program. ; _item.name '_phasing_averaging.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Iterative 3-fold averaging alternating with phase extension by 0.5 reciprocal lattice units per cycle according to the method described by X and Y (ref). ;
_category.description ; Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure, when a model isomorphous to the structure being phased was used to generate initial phases. ; _category.id _category.id _category.mandatory_code no _category_key.name '_phasing_isomorphous.block_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 4PHV and laboratory records for the structure corresponding to PDB entry 4PHV ; ; _phasing_isomorphous.parent 'PDB entry 5HVP' _phasing_isomorphous.details ; The inhibitor and all solvent atoms were removed from the parent structure before beginning refinement. All static disorder present in the parent structure was also removed. ; ;
save_phasing_isomorphous.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_phasing_isomorphous.details.
_item_description.description ; A description of special aspects of the isomorphous phasing. ; _item.name '_phasing_isomorphous.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Residues 13-18 were eliminated from the starting model as it was anticipated that binding of the inhibitor would cause a structural rearrangement in this part of the structure. ;
save_phasing_isomorphous.method.
_item_description.description ; A description of the isomorphous phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the _computing. data items. Rather this data item should be used to describe significant methodological options used within the isomorphous phasing program. ; _item.name '_phasing_isomorphous.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Iterative 3-fold averaging alternating with phase extension by 0.5 reciprocal lattice units per cycle according to the method described by X and Y (ref). ;
save_phasing_isomorphous.parent.
_item_description.description ; Reference to the structure used to generate starting phases if the structure referenced in this data block was phased by virtue of being isomorphous to a known structure (e.g., a mutant that crystallizes in the same space group as the wild type protein.) ; _item.name '_phasing_isomorphous.parent' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the PHASING_MAD category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved. ; _category.id _category.id _category.mandatory_code no _category_key.name '_phasing_MAD.block_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; A description of special aspects of the MAD phasing. ; _item.name '_phasing_MAD.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; A description of the MAD phasing method applied to phase this structure. Note that this is not the computer program used, which is described in _computing.phasing_MAD. Rather this data item should be used to describe significant methodological options used within the MAD phasing program. ; _item.name '_phasing_MAD.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the PHASING_MIR category record details about the phasing of the structure, when methods involving isomorphous replacement are involved. All isomorphous based techniques are subsumed in this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR), single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS). ; _category.id _category.id _category.mandatory_code no _category_key.name '_phasing_MIR.block_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993) ; ; _phasing_MIR.method ; Standard phase refinement (Blow and Crick, 1959) ; ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; A description of special aspects of the isomorphous phasing. ; _item.name '_phasing_MIR.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in _computing.phasing_MIR. Rather this data item should be used to describe significant methodological options used within the MIR phasing program. ; _item.name '_phasing_MIR.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. ; _category.id _category.id _category.mandatory_code no _category_key.name '_phasing_MIR_der.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993) ; ; loop_ _phasing_MIR_der.id _phasing_MIR_der.number_of_sites _phasing_MIR_der.details KAu(CN)2 3 'major site interpreted in difference Patterson' K2HgI4 6 'sites found in cross-difference Fourier' K3IrCl6 2 'sites found in cross-difference Fourier' All 11 'data for all three derivatives combined' ;
_item_description.description ; A description of special aspects of this derivative, its data, its solution, or its use in phasing. ; _item.name '_phasing_MIR_der.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; The value of _phasing_MIR_der.id must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MIR_der.id' phasing_MIR_der yes '_phasing_MIR_refln.der_id' phasing_MIR_refln yes '_phasing_MIR_site.der_id' phasing_MIR_site yes '_phasing_MIR_der_shell.der_id' phasing_MIR_der_shell yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MIR_refln.der_id' '_phasing_MIR_der.id' '_phasing_MIR_site.der_id' '_phasing_MIR_der.id' '_phasing_MIR_der_shell.der_id' '_phasing_MIR_der.id' _item_type.code char loop_ _item_examples.case 'KAu(CN)2' K2HgI4
save_phasing_MIR_der.number_of_sites.
_item_description.description ; The number of heavy atom sites in this derivative. ; _item.name '_phasing_MIR_der.number_of_sites' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_phasing_MIR_der.reflns_criteria.
_item_description.description ; Criteria used to limit the reflections used in the phasing calculations. ; _item.name '_phasing_MIR_der.reflns_criteria' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case '> 4 \s(I)'
_category.description ; Data items in the PHASING_MIR_DER_SHELL category record details for each derivative, broken down into shells of resolution, when the phasing method involves isomorphous replacement. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_der_shell.der_id' '_phasing_MIR_der_shell.d_res_low' '_phasing_MIR_der_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993) made up arbitrary low-resolution limit ; ; loop_ _phasing_MIR_der_shell.der_id _phasing_MIR_der_shell.d_res_low _phasing_MIR_der_shell.d_res_high _phasing_MIR_der_shell.ha_ampl _phasing_MIR_der_shell.loc KAu(CN)2 15.0 8.3 54 26 KAu(CN)2 8.3 6.4 54 20 KAu(CN)2 6.4 5.2 50 20 KAu(CN)2 5.2 4.4 44 23 KAu(CN)2 4.4 3.8 39 23 KAu(CN)2 3.8 3.4 33 21 KAu(CN)2 3.4 3.0 28 17 KAu(CN)2 15.0 3.0 38 21 K2HgI4 15.0 8.3 149 87 K2HgI4 8.3 6.4 121 73 K2HgI4 6.4 5.2 95 61 K2HgI4 5.2 4.4 80 60 K2HgI4 4.4 3.8 73 63 K2HgI4 3.8 3.4 68 57 K2HgI4 3.4 3.0 63 46 K2HgI4 15.0 3.0 79 58 K3IrCl6 15.0 8.3 33 27 K3IrCl6 8.3 6.4 40 23 K3IrCl6 6.4 5.2 31 22 K3IrCl6 5.2 4.4 27 23 K3IrCl6 4.4 3.8 22 23 K3IrCl6 3.8 3.4 19 20 K3IrCl6 3.4 3.0 16 20 K3IrCl6 15.0 3.0 23 21 ;
save_phasing_MIR_der_shell.d_res_high.
_item_description.description ; The highest resolution for the interplanar spacing in the reflection data for this derivative in this shell. This is the smallest d value. ; _item.name '_phasing_MIR_der_shell.d_res_high' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_der_shell.d_res_low.
_item_description.description ; The lowest resolution for the interplanar spacing in the reflection data for this derivative in this shell. This is the highest d value. ; _item.name '_phasing_MIR_der_shell.d_res_low' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_der_shell.der_id.
_item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ;
save_phasing_MIR_der_shell.fom.
_item_description.description ; The mean value of the figure of merit m for reflections for this derivative in this shell. int P(a) exp(ia) da m = ------------------- int P(a) da where P(a) is the probability that phase angle a is correct and the integrals are taken over the range a = 0 to 2 pi. ; _item.name '_phasing_MIR_der_shell.fom' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_der_shell.ha_ampl.
_item_description.description ; The mean heavy-atom amplitude for reflections in this derivative in this shell. ; _item.name '_phasing_MIR_der_shell.ha_ampl' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_der_shell.loc.
_item_description.description ; The mean lack-of-closure error for reflections in this derivative in this shell. Lack-of-closure = Sum |F~ph~(obs) - F~ph~(calc)| where F~ph~(obs) and F~ph~(calc) are the observed and calculated structure factor amplitudes of the derivative. ; _item.name '_phasing_MIR_der_shell.loc' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_der_shell.phase.
_item_description.description ; The mean of the phase values for reflections in this derivative in this shell. ; _item.name '_phasing_MIR_der_shell.phase' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_phasing_MIR_der_shell.power.
_item_description.description ; The mean phasing power for reflections in this derivative in this shell. { Sum F~h~(calc)^2^ }^1/2^ Phasing power = { --------------------------------- } { Sum |F~ph~(obs) - F~ph~(calc)|^2^ } where F~h~(calc) is the calculated structure factor amplitude of the heavy atom and F~ph~(obs) and F~ph~(calc) are the observed and calculated structure factor amplitudes of the derivative. ; _item.name '_phasing_MIR_der_shell.power' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_der_shell.R_Cullis.
_item_description.description ; The R-factor for centric reflections in this derivative in this shell. R-Cullis: Sum ||F~ph~(obs)+/-F~p~(obs)|-F~h~(calc)| / Sum | F~ph~(obs)-F~p~(obs)| where F~p~(obs) is the observed structure factor amplitude of the parent molecule, F~h~(calc) is the calculated structure factor amplitude of the heavy atom and F~ph~(obs) is the observed structure factor amplitude of the derivative. Cullis A F, Muirhead H, Perutz M F, Rossmann M G and North A C T (1961) Proc. Roy. Soc. A265, 15-38. ; _item.name '_phasing_MIR_der_shell.R_Cullis' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_der_shell.R_Kraut.
_item_description.description ; The R-factor for general reflections in this derivative in this shell. Sum |F~ph~(obs)-F~ph~(calc)| R-Kraut = ---------------------------- Sum |F~ph~(obs)| where F~ph~(obs) and F~ph~(calc) are the observed and calculated structure factor amplitudes of the derivative. Kraut, J., Sieker, L.C., High, D.F. and Freer, S.T. (1962). Proc. Natl. Acad. Sci. USA, Vol 48, p. 1417. ; _item.name '_phasing_MIR_der_shell.R_Kraut' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_der_shell.reflns.
_item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_der_shell.reflns' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_category.description ; Data items in the PHASING_MIR_REFLN category record details about the reflection data used in an MIR experiment. This category of data items is provided so that derivative intensity and phase information can be stored in the same data block as the native information. However, no provision is made for the storage of all of the details of obtaining those data; to store such detailed information a separate data block should be used for each derivative. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_refln.index_h' '_phasing_MIR_refln.index_k' '_phasing_MIR_refln.index_l' '_phasing_MIR_refln.der_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993) ; ; Need Example 1 ;
save_phasing_MIR_refln.A_calc.
_item_description.description ; The calculated value of structure-factor component A for this derivative, in electrons. A = |F|cos(phase) ; _item.name '_phasing_MIR_refln.A_calc' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'electrons'
save_phasing_MIR_refln.A_meas.
_item_description.description ; The measured value of structure-factor component A for this derivative, in electrons. A = |F|cos(phase) ; _item.name '_phasing_MIR_refln.A_meas' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'electrons'
save_phasing_MIR_refln.B_calc.
_item_description.description ; The calculated value of structure-factor component B for this derivative, in electrons. B = |F|sin(phase) ; _item.name '_phasing_MIR_refln.B_calc' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'electrons'
save_phasing_MIR_refln.B_meas.
_item_description.description ; The measured value of structure-factor component B for this derivative, in electrons. B = |F|sin(phase) ; _item.name '_phasing_MIR_refln.B_meas' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'electrons'
save_phasing_MIR_refln.der_id.
_item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ;
save_phasing_MIR_refln.F_calc.
_item_description.description ; The calculated value of the structure factor for this derivative, in electrons. ; _item.name '_phasing_MIR_refln.F_calc' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'electrons'
save_phasing_MIR_refln.F_meas.
_item_description.description ; The measured value of the structure factor for this derivative, in electrons. ; _item.name '_phasing_MIR_refln.F_meas' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'electrons'
save_phasing_MIR_refln.F_sigma.
_item_description.description ; The standard deviation (derived from the measured value) of the structure factor for this derivative, in electrons. ; _item.name '_phasing_MIR_refln.F_sigma' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'electrons'
save_phasing_MIR_refln.HL_A_iso.
_item_description.description ; The isomorphous Hendrickson-Lattman coefficient Aiso for this reflection for this derivative. -2.0 * (Fp^2 + Fh^2 - Fph^2) * Fp * cos(alphah) Aiso = ---------------------------------------------- E^2 where Fp = the structure factor amplitude of the native Fph = the structure factor amplitude of the derivative Fh = the structure factor amplitude calculated from the heavy atom model alphah = the phase calculated from the heavy atom model E = ((Fph - Fp) - Fh)^2 for centric reflections = ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections ; _item.name '_phasing_MIR_refln.HL_A_iso' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_phasing_MIR_refln.HL_B_iso.
_item_description.description ; The isomorphous Hendrickson-Lattman coefficient Biso for this reflection for this derivative. -2.0 * (Fp^2 + Fh^2 - Fph^2) * Fp * sin(alphah) Biso = ---------------------------------------------- E^2 where Fp = the structure factor amplitude of the native Fph = the structure factor amplitude of the derivative Fh = the structure factor amplitude calculated from the heavy atom model alphah = the phase calculated from the heavy atom model E = ((Fph - Fp) - Fh)^2 for centric reflections = ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections ; _item.name '_phasing_MIR_refln.HL_B_iso' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_phasing_MIR_refln.HL_C_iso.
_item_description.description ; The isomorphous Hendrickson-Lattman coefficient Ciso for this reflection for this derivative. -Fp^2 * (sin(alphah)^2 - cos(alphah)^2) Ciso = --------------------------------------- E^2 where Fp = the structure factor amplitude of the native Fph = the structure factor amplitude of the derivative Fh = the structure factor amplitude calculated from the heavy atom model alphah = the phase calculated from the heavy atom model E = ((Fph - Fp) - Fh)^2 for centric reflections = ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections ; _item.name '_phasing_MIR_refln.HL_C_iso' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_phasing_MIR_refln.HL_D_iso.
_item_description.description ; The isomorphous Hendrickson-Lattman coefficient Diso for this reflection for this derivative. -2.0 * Fp^2 * sin(alphah)^2 * cos(alphah)^2 Diso = ------------------------------------------- E^2 where Fp = the structure factor amplitude of the native Fph = the structure factor amplitude of the derivative Fh = the structure factor amplitude calculated from the heavy atom model alphah = the phase calculated from the heavy atom model E = ((Fph - Fp) - Fh)^2 for centric reflections = ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections ; _item.name '_phasing_MIR_refln.HL_D_iso' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_phasing_MIR_refln.index_h.
_item_description.description ; Miller index h of the reflection. ; _item.name '_phasing_MIR_refln.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' loop_ _item_dependent.dependent_name '_phasing_MIR_refln.index_k' '_phasing_MIR_refln.index_l' _item_type.code int
save_phasing_MIR_refln.index_k.
_item_description.description ; Miller index h of the reflection. ; _item.name '_phasing_MIR_refln.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' loop_ _item_dependent.dependent_name '_phasing_MIR_refln.index_h' '_phasing_MIR_refln.index_l' _item_type.code int
save_phasing_MIR_refln.index_l.
_item_description.description ; Miller index h of the reflection. ; _item.name '_phasing_MIR_refln.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' loop_ _item_dependent.dependent_name '_phasing_MIR_refln.index_h' '_phasing_MIR_refln.index_k' _item_type.code int
save_phasing_MIR_refln.phase_calc.
_item_description.description ; The calculated value of the structure-factor phase for this derivative, in degrees. ; _item.name '_phasing_MIR_refln.phase_calc' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
save_phasing_MIR_refln.phase_meas.
_item_description.description ; The measured value of the structure-factor phase for this derivative, in degrees. ; _item.name '_phasing_MIR_refln.phase_meas' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_category.description ; Data items in the PHASING_MIR_SHELL category record details broken down into shells of resolution, when the phasing method involves isomorphous replacement. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_shell.d_res_low' '_phasing_MIR_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993) made up arbitrary low-resolution limit ; ; loop_ _phasing_MIR_shell.d_res_low _phasing_MIR_shell.d_res_high _phasing_MIR_shell.reflns _phasing_MIR_shell.fom 15.0 8.3 80 0.69 8.3 6.4 184 0.73 6.4 5.2 288 0.72 5.2 4.4 406 0.65 4.4 3.8 554 0.54 3.8 3.4 730 0.53 3.4 3.0 939 0.50 ;
save_phasing_MIR_shell.d_res_high.
_item_description.description ; The highest resolution for the interplanar spacing in the reflection data in this shell. This is the smallest d value. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. ; _item.name '_phasing_MIR_shell.d_res_high' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_shell.d_res_low.
_item_description.description ; The lowest resolution for the interplanar spacing in the reflection data in this shell. This is the largest d value. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. ; _item.name '_phasing_MIR_shell.d_res_low' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; The mean value of the figure of merit m for reflections in this shell. int P(a) exp(ia) da m = ------------------- int P(a) da where P(a) is the probability that phase angle a is correct and the integrals are taken over the range a = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.fom' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description ; The mean lack-of-closure error for reflections in this shell. Lack-of-closure = Sum |F~ph~(obs) - F~ph~(calc)| where F~ph~(obs) and F~ph~(calc) are the observed and calculated structure factor amplitudes of the derivative. ; _item.name '_phasing_MIR_shell.loc' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_shell.mean_phase.
_item_description.description ; The mean of the phase values for all reflections in this shell. ; _item.name '_phasing_MIR_shell.mean_phase' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description ; The mean phasing power for reflections in this shell. { Sum F~h~(calc)^2^ }^1/2^ Phasing power = { --------------------------------- } { Sum |F~ph~(obs) - F~ph~(calc)|^2^ } where F~h~(calc) is the calculated structure factor amplitude of the heavy atom and F~ph~(obs) and F~ph~(calc) are the observed and calculated structure factor amplitudes of the derivative. ; _item.name '_phasing_MIR_shell.power' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_shell.R_Cullis.
_item_description.description ; The R-factor for centric reflections in this shell. R-Cullis: Sum ||F~ph~(obs)+/-F~p~(obs)|-F~h~(calc)| / Sum | F~ph~(obs)-F~p~(obs)| where F~p~(obs) is the observed structure factor amplitude of the parent molecule, F~h~(calc) is the calculated structure factor amplitude of the heavy atom and F~ph~(obs) is the observed structure factor amplitude of the derivative. Cullis et al. (1961) Proc. Roy. Soc. A265, 15-??. ; _item.name '_phasing_MIR_shell.R_Cullis' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_shell.R_Kraut.
_item_description.description ; The R-factor for general reflections in this shell. Sum |F~ph~(obs)-F~ph~(calc)| R-Kraut = ---------------------------- Sum |F~ph~(obs)| where F~ph~(obs) and F~ph~(calc) are the observed and calculated structure factor amplitudes of the derivative. Kraut, J., Sieker, L.C., High, D.F. and Freer, S.T. (1962). Proc. Natl. Acad. Sci. USA, Vol 48, p. 1417. ; _item.name '_phasing_MIR_shell.R_Kraut' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_phasing_MIR_shell.reflns.
_item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_category.description ; Data items in the PHASING_MIR_SITE category record details about the heavy-atom sites, when the phasing method involves isomorphous replacement. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_site.der_id' '_phasing_MIR_site.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993) with occupancies converted from electrons to fractional ; ; loop_ _phasing_MIR_site.der_id _phasing_MIR_site.id _phasing_MIR_site.atom_type_symbol _phasing_MIR_site.occupancy _phasing_MIR_site.fract_x _phasing_MIR_site.fract_y _phasing_MIR_site.fract_z _phasing_MIR_site.B_iso KAu(CN)2 1 Au 0.40 0.082 0.266 0.615 33.0 KAu(CN)2 2 Au 0.03 0.607 0.217 0.816 25.9 KAu(CN)2 3 Au 0.02 0.263 0.782 0.906 15.7 K2HgI4 1 Hg 0.63 0.048 0.286 0.636 33.7 K2HgI4 2 Hg 0.34 0.913 0.768 0.889 36.7 K2HgI4 3 Hg 0.23 0.974 0.455 0.974 24.2 K2HgI4 4 Hg 0.28 0.903 0.836 0.859 14.7 K2HgI4 5 Hg 0.07 0.489 0.200 0.885 6.4 K2HgI4 6 Hg 0.07 0.162 0.799 0.889 32.9 K3IrCl6 1 Ir 0.26 0.209 0.739 0.758 40.8 K3IrCl6 2 Ir 0.05 0.279 0.613 0.752 24.9 ;
save_phasing_MIR_site.atom_type_symbol.
_item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. The scattering factors referenced via this data item should be those used in the refinement of the heavy atom data; in some cases this will be the scattering factor to the single heavy atom, in others it will be scattering factors for an atomic cluster. ;
_item_description.description ; Isotropic temperature factor for this heavy-atom site in this derivative. ; _item.name '_phasing_MIR_site.B_iso' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms' _esd_default 0.0
save_phasing_MIR_site.B_iso_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.B_iso. ; _item.name '_phasing_MIR_site.B_iso_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_x.
_item_description.description ; The x coordinate of this heavy-atom position in this derivative specified as orthogonal Angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.cartn_transform_axes. ; _item.name '_phasing_MIR_site.cartn_x' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_y' '_phasing_MIR_site.cartn_z' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_x_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.cartn_x. ; _item.name '_phasing_MIR_site.cartn_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_y_esd' '_phasing_MIR_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_y.
_item_description.description ; The y coordinate of this heavy-atom position in this derivative specified as orthogonal Angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.cartn_transform_axes. ; _item.name '_phasing_MIR_site.cartn_y' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_x' '_phasing_MIR_site.cartn_z' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_y_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.cartn_y. ; _item.name '_phasing_MIR_site.cartn_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_x_esd' '_phasing_MIR_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_z.
_item_description.description ; The z coordinate of this heavy-atom position in this derivative specified as orthogonal Angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.cartn_transform_axes. ; _item.name '_phasing_MIR_site.cartn_z' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate' loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_x' '_phasing_MIR_site.cartn_y' _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_z_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.cartn_z. ; _item.name '_phasing_MIR_site.cartn_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_x_esd' '_phasing_MIR_site.cartn_y_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ;
save_phasing_MIR_site.details.
_item_description.description ; A description of special aspects of the derivative site. ; _item.name '_phasing_MIR_site.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'binds to His 117' 'minor site obtained from difference Fourier' 'same as site 2 in the K2HgI4 derivative'
save_phasing_MIR_site.fract_x.
_item_description.description ; The x coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_a. ; _item.name '_phasing_MIR_site.fract_x' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate' loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_y' '_phasing_MIR_site.fract_z' _item_type.code float _item_type_conditions.code esd
save_phasing_MIR_site.fract_x_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.fract_x. ; _item.name '_phasing_MIR_site.fract_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_y_esd' '_phasing_MIR_site.fract_z_esd' _item_type.code float
save_phasing_MIR_site.fract_y.
_item_description.description ; The y coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_b. ; _item.name '_phasing_MIR_site.fract_y' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate' loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_x' '_phasing_MIR_site.fract_z' _item_type.code float _item_type_conditions.code esd
save_phasing_MIR_site.fract_y_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.fract_y. ; _item.name '_phasing_MIR_site.fract_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_x_esd' '_phasing_MIR_site.fract_z_esd' _item_type.code float
save_phasing_MIR_site.fract_z.
_item_description.description ; The z coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_c. ; _item.name '_phasing_MIR_site.fract_z' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate' loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_x' '_phasing_MIR_site.fract_y' _item_type.code float _item_type_conditions.code esd
save_phasing_MIR_site.fract_z_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.fract_z. ; _item.name '_phasing_MIR_site.fract_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_x_esd' '_phasing_MIR_site.fract_y_esd' _item_type.code float
_item_description.description ; The value of _phasing_MIR_site.id must uniquely identify each site in each derivative in the PHASING_MIR_SITE list. The atom identifiers need not be unique over all sites in all derivatives; they need only be unique for each site in each derivative. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_phasing_MIR_site.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
save_phasing_MIR_site.occupancy.
_item_description.description ; The fraction of the atom type present at this heavy-atom site in a given derivative. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. ; _item.name '_phasing_MIR_site.occupancy' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1.0 _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_category.description ; Data items in the PHASING_MR category record details about the phasing of the structure, when methods involving molecular replacement are involved. ; _category.id _category.id _category.mandatory_code no _category_key.name '_phasing_MR.block_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; A description of the molecular replacement phasing method applied to phase this structure. Note that this is not the computer program used, which is described in _computing.phasing_MR. Rather this data item should be used to describe significant methodological options used within the molecular replacement phasing program. ; _item.name '_phasing_MR.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the PUBL category are used when submitting a manuscript for publication. ; _category.id _category.id _category.mandatory_code no _category_key.name '_publ.block_id' loop_ _category_group.id 'inclusive_group' 'publ_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _publ.section_title ; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-1,3-oxazolidin-5-one ; _publ.section_abstract ; The oxazolidinone ring is a shallow envelope conformation with the tert-butyl and iso-butyl groups occupying trans-positions with respect to the ring. The angles at the N atom sum to 356.2\%, indicating a very small degree of pyramidalization at this atom. This is consistent with electron delocalization between the N atom and the carbonyl centre [N-C=O = 1.374(3)\%A]. ; ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The name and address of the author submitting the manuscript and CIF. This is the person contacted by the journal editorial staff. ; _item.name '_publ.contact_author' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author' _item_type.code char _item_examples.case ; Professor Dr. J.U. Blogs Department of Structural Chemistry RRDD Institute of Technology Building #6-M57 Highho Street Citytown 64664 COUNTRYHERE ;
save_publ.contact_author_email.
_item_description.description ; Email address in a form recognisable to international networks. ; _item.name '_publ.contact_author_email' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_email' _item_type.code char loop_ _item_examples.case name@host.domain.country uur5@banjo.bitnet
_item_description.description ; Facsimile telephone number with international code in parentheses. ; _item.name '_publ.contact_author_fax' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_fax' _item_type.code char _item_examples.case '(12) 34 947 7334'
save_publ.contact_author_phone.
_item_description.description ; Telephone number with international code in parentheses and any extension number preceded by 'ext'. ; _item.name '_publ.contact_author_phone' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_phone' _item_type.code char _item_examples.case '(12) 34 947 7330 ext 5543'
_item_description.description ; A letter submitted to the journal editor by the contact author. ; _item.name '_publ.contact_letter' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_contact_letter' _item_type.code char
save_publ.manuscript_creation.
_item_description.description ; A description of the wordprocessor package and computer used to create the word processed manuscript stored as _publ_manuscript_processed. ; _item.name '_publ.manuscript_creation' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_creation' _item_type.code char _item_examples.case 'Tex file created by FrameMaker on a Sun 3/280'
save_publ.manuscript_processed.
_item_description.description ; The full manuscript of a paper (excluding possibly the figures and the tables) output in ASCII characters from a word processor. Information about the generation of this data item must be specified in the data item _publ_manuscript_creation. ; _item.name '_publ.manuscript_processed' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_processed' _item_type.code char
_item_description.description ; The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text. ; _item.name '_publ.manuscript_text' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_text' _item_type.code char
save_publ.requested_coeditor_name.
_item_description.description ; The Co-editor's name requested to process the submitted manuscript. ; _item.name '_publ.requested_coeditor_name' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_requested_coeditor_name' _item_type.code char
_item_description.description ; The journal's name requested for publication. ; _item.name '_publ.requested_journal' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_requested_journal' _item_type.code char
_item_description.description ; The abstract section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_abstract' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_abstract' _item_type.code char
save_publ.section_acknowledgements.
_item_description.description ; The acknowledgements section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_acknowledgements' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_acknowledgements' _item_type.code char
_item_description.description ; The comment section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_comment' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_comment' _item_type.code char
_item_description.description ; The discussion section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_discussion' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_discussion' _item_type.code char
save_publ.section_experimental.
_item_description.description ; The experimental section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. The _publ.section_exptl_prep and _publ.section_exptl_refinement items are preferred for separating the chemical preparation and refinement aspects of the experimental description. ; _item.name '_publ.section_experimental' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_experimental' _item_type.code char
_item_description.description ; The experimental preparation section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_exptl_prep' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_prep' _item_type.code char
save_publ.section_exptl_refinement.
_item_description.description ; The experimental refinement section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_exptl_refinement' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_refinement' _item_type.code char
save_publ.section_figure_captions.
_item_description.description ; The figure captions section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_figure_captions' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_figure_captions' _item_type.code char
save_publ.section_introduction.
_item_description.description ; The introduction section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_introduction' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_introduction' _item_type.code char
_item_description.description ; The references section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_references' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_references' _item_type.code char
save_publ.section_table_legends.
_item_description.description ; The table legends captions section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_table_legends' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_table_legends' _item_type.code char
_item_description.description ; The title section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. ; _item.name '_publ.section_title' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_section_title' _item_type.code char
_category.description ; Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication. ; _category.id _category.id _category.mandatory_code no _category_key.name '_publ_author.name' loop_ _category_group.id 'inclusive_group' 'publ_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _publ_author.name _publ_author.address 'Willis, Anthony C.' ; Research School of Chemistry Australian National University GPO Box 4 Canberra, A.C.T. Australia 2601 ; ;
_item_description.description ; The address of a publication author. If there is more than one author this will be looped with _publ_author_name. ; _item.name '_publ_author.address' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_author_address' _item_type.code char _item_examples.case ; Department Institute Street City and postcode COUNTRY ;
_item_description.description ; The name of a publication author. If there are multiple authors they will be looped with _publ_author_address. The family name(s) followed by a comma, precedes the first names or initials. ; _item.name '_publ_author.name' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_author_name' _item_type.code char loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A'
_category.description ; Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list employed by journal printing software. ; _category.id _category.id _category.mandatory_code no _category_key.name '_publ_manuscript_incl.block_id' loop_ _category_group.id 'inclusive_group' 'publ_group' loop_ _category_examples.detail _category_examples.case ; Example 2 - Example is completely hypothetical. ; ; loop_ _publ_manuscript_incl.extra_item _publ_manuscript_incl.extra_info _publ_manuscript_incl.extra_defn '_atom_site_symmetry_multiplicity' 'to emphasise very special sites' yes '_chemical_compound_source' 'rare material from unusual source' yes '_reflns_d_resolution_high' 'the limited data is a problem here' yes '_crystal_magnetic_permeability' 'a new data quantity needed here' no ;
save_publ_manuscript_incl.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_publ_manuscript_incl.extra_defn.
_item_description.description ; Specifies whether or not the extra information being included into a manuscript is a standard definition. ; _item.name '_publ_manuscript_incl.extra_defn' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_defn' _item_type.code char loop_ _item_examples.case yes no
save_publ_manuscript_incl.extra_info.
_item_description.description ; Specifies the reason for including extra information into a manuscript. ; _item.name '_publ_manuscript_incl.extra_info' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_info' _item_type.code char loop_ _item_examples.case 'to emphasise very special sites' 'rare material from unusual source' 'the limited data is a problem here' 'a new data quantity needed here'
save_publ_manuscript_incl.extra_item.
_item_description.description ; Specifies the name of a data item used to include extra information into a manuscript. Note that _publ_manuscript_incl.extra_item names MUST be enclosed in single quotes. ; _item.name '_publ_manuscript_incl.extra_item' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_item' _item_type.code char loop_ _item_examples.case '_atom_site_symmetry_multiplicity' '_chemical_compound_source' '_reflns_d_resolution_high' '_crystal_magnetic_permeability'
_category.description ; Data items in the REFINE category record details about the structure refinement parameters. ; _category.id _category.id _category.mandatory_code no _category_key.name '_refine.block_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _refine.ls_number_reflns_obs 12901 _refine.ls_number_restraints 6609 _refine.ls_number_parameters 7032 _refine.ls_R_Factor_obs 0.176 _refine.ls_weighting_scheme calc _refine.ls_weighting_details ; Sigdel model of Konnert-Hendrickson: Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = -150.0 at the beginning of refinement. Afsig = 15.5, Bfsig = -50.0 at the end of refinement. ; ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _refine.details sfls:_F_calc_weight_full_matrix _refine.ls_structure_factor_coef F _refine.ls_matrix_type full _refine.ls_weighting_scheme 'calc w=1/(\s^2^(F)+0.0004F^2^)' _refine.ls_hydrogen_treatment 'refxyz except H332B noref' _refine.ls_extinction_method Zachariasen _refine.ls_extinction_coef 3514(42) _refine.ls_extinction_expression 'equ(22) p292 "Crystallographic Computing" (1970)' _refine.ls_abs_structure_details ; The absolute configuration was assigned to agree with the known chirality at C3 arising from its precursor l-leucine. ; _refine.ls_abs_structure_Flack 0 _refine.ls_number_reflns_obs 1408 _refine.ls_number_parameters 272 _refine.ls_number_restraints 0 _refine.ls_number_constraints 0 _refine.ls_R_factor_all .038 _refine.ls_R_factor_obs .034 _refine.ls_wR_factor_all .044 _refine.ls_wR_factor_obs .042 _refine.ls_goodness_of_fit_all 1.462 _refine.ls_goodness_of_fit_obs 1.515 _refine.ls_shift/esd_max .535 _refine.ls_shift/esd_mean .044 _refine.diff_density_min -.108 _refine.diff_density_max .131 ;
_item_description.description ; The maximum value for isotropic B value (temperature factors) found in the coordinate set. ; _item.name '_refine.B_iso_max' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'angstroms_squared'
_item_description.description ; The minimum value for isotropic B value (temperature factors) found in the coordinate set. ; _item.name '_refine.B_iso_min' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'angstroms_squared'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; Description of special aspects of the refinement process. ; _item.name '_refine.details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_special_details' _item_type.code char
_item_description.description ; The maximum value of the electron density in the final difference Fourier map. ; _item.name '_refine.diff_density_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_max' _item_type.code float _item_type_conditions.code esd _item_units.code 'electrons_per_angstroms_cubed'
save_refine.diff_density_max_esd.
_item_description.description ; The estimated standard deviation of _refine.diff_density_max. ; _item.name '_refine.diff_density_max_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'electrons_per_angstroms_cubed'
_item_description.description ; The minimum value of the electron density in the final difference Fourier map. ; _item.name '_refine.diff_density_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_min' _item_type.code float _item_type_conditions.code esd _item_units.code 'electrons_per_angstroms_cubed'
save_refine.diff_density_min_esd.
_item_description.description ; The estimated standard deviation of _refine.diff_density_min. ; _item.name '_refine.diff_density_min_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'electrons_per_angstroms_cubed'
_item_description.description ; The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density, and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels. ; _item.name '_refine.diff_density_rms' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_rms' _item_type.code float _item_type_conditions.code esd _item_units.code 'electrons_per_angstroms_cubed'
save_refine.diff_density_rms_esd.
_item_description.description ; The estimated standard deviation of _refine.diff_density_rms. ; _item.name '_refine.diff_density_rms_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'electrons_per_angstroms_cubed'
save_refine.ls_abs_structure_details.
_item_description.description ; The nature of the absolute structure and how it was determined. For example, to describe the nature of the Friedel data used. ; _item.name '_refine.ls_abs_structure_details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_details' _item_type.code char
save_refine.ls_abs_structure_Flack.
_item_description.description ; This measure of absolute structure (enantiomorph or polarity) is defined in the paper by Flack, H. D. (1983). Acta Cryst. A39, 876-881. The value must be between 0. and 1. with an e.s.d. ; _item.name '_refine.ls_abs_structure_Flack' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_Flack' _item_type.code float _item_type_conditions.code esd
save_refine.ls_abs_structure_Flack_esd.
_item_description.description ; The estimated standard deviation of _refine.ls_abs_structure_Flack. ; _item.name '_refine.ls_abs_structure_Flack_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_refine.ls_abs_structure_Rogers.
_item_description.description ; This measure of absolute structure (enantiomorph or polarity) is defined in the paper by Rogers, D. (1981). Acta Cryst. A37, 734-741. ; _item.name '_refine.ls_abs_structure_Rogers' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_Rogers' _item_type.code float _item_type_conditions.code esd
save_refine.ls_abs_structure_Rogers_esd.
_item_description.description ; The estimated standard deviation of _refine.ls_abs_structure_Rogers. ; _item.name '_refine.ls_abs_structure_Rogers_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_refine.ls_extinction_coef.
_item_description.description ; The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of _refine.ls_extinction_expression & _refine.ls_extinction_method. For the 'Zachariasen' method it will be the r* value; for the 'B-C type 1 isotropic' method it is the 'g' value, and for 'B-C type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. ; _item.name '_refine.ls_extinction_coef' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_coef' _item_type.code float _item_type_conditions.code esd _item_examples.case 3472(52) _item_examples.detail 'Zachariasen coefficient r* = 0.347(5) E04'
save_refine.ls_extinction_coef_esd.
_item_description.description ; The estimated standard deviation of _refine.ls_extinction_coef. ; _item.name '_refine.ls_extinction_coef_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_refine.ls_extinction_expression.
_item_description.description ; A description or reference of the extinction correction equation used to apply the data item _refine.ls_extinction_coef. This information must be sufficient to reproduce the extinction correction factors applied to the structure factors. ; _item.name '_refine.ls_extinction_expression' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Equation (22) p292 "Crystallographic Computing" Munksgaard 1970 ;
save_refine.ls_extinction_method.
_item_description.description ; A description of the extinction correction method applied with the data item _refine.ls_extinction_coef. This description should include information about the correction method 'Becker-Coppens' [Becker, P.J. & Coppens, P. (1974) Acta Cryst. A30, 129-153] or 'Zachariasen' [Zachariasen, W.H. (1967) Acta Cryst. 23, 558- 564]. The latter is sometimes referred to as the 'Larson' method [Larson, A.C. (1967) Acta Cryst. 23, 664-665] even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the B-C method it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian'; and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied the multiple coefficients cannot be contained in *_extinction_coef and must be listed in _refine.details. ; _item.name '_refine.ls_extinction_method' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_method' _item_default.value 'Zachariasen' _item_type.code char _item_examples.case 'B-C type 2 Gaussian isotropic'
save_refine.ls_goodness_of_fit_all.
_item_description.description ; The least-squares goodness-of-fit parameter S for all data, after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. S = [sum(w|Ym-Yc|^2^) / (Nref-Nparam)]^1/2^ where the sum is over the specified reflection data; Nref is the number of reflections used in the refinement; Nparam is the number of refined parameters; Ym and Yc are the measured and calculated coefficients specified in _refine.ls_structure_factor_coef; and w is the least-squares weight [1/(e.s.d. squared)]. See also the definition of _refine.ls_restrained_S_all. ; _item.name '_refine.ls_goodness_of_fit_all' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_goodness_of_fit_all' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd
save_refine.ls_goodness_of_fit_all_esd.
_item_description.description ; The estimated standard deviation of _refine.ls_goodness_of_fit_all. ; _item.name '_refine.ls_goodness_of_fit_all_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_refine.ls_goodness_of_fit_obs.
_item_description.description ; The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see _reflns_observed_criterion), after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. S = [sum(w|Ym-Yc|^2^) / (Nref-Nparam)]^1/2^ where the sum is over the specified reflection data; Nref is the number of reflections used in the refinement; Nparam is the number of refined parameters; Ym and Yc are the measured and calculated coefficients specified in _refine.ls_structure_factor_coef; and w is the least-squares weight [1/(e.s.d. squared)]. See also the definition of _refine.ls_restrained_S_obs. ; _item.name '_refine.ls_goodness_of_fit_obs' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_goodness_of_fit_obs' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd
save_refine.ls_goodness_of_fit_obs_esd.
_item_description.description ; The estimated standard deviation of _refine.ls_goodness_of_fit_obs. ; _item.name '_refine.ls_goodness_of_fit_obs_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_refine.ls_hydrogen_treatment.
_item_description.description ; Treatment of hydrogen atoms in the least-squares refinement. ; _item.name '_refine.ls_hydrogen_treatment' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_hydrogen_treatment' _item_default.value undef _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail refall 'refined all H parameters' refxyz 'refined H coordinates only' refU 'refined H U only' noref 'no refinement of H parameters' undef 'not defined'
_item_description.description ; Type of matrix used to accumulate the least-squares derivatives. ; _item.name '_refine.ls_matrix_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_matrix_type' _item_default.value full _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail full 'full' fullcycle 'full with fixed elements per cycle' atomblock 'block diagonal per atom' userblock 'user-defined blocks' diagonal 'diagonal elements only' sparse 'selected elements only'
save_refine.ls_number_constraints.
_item_description.description ; The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site_refinement_flags. A general description of constraints may appear in _refine.details. ; _item.name '_refine.ls_number_constraints' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_constraints' _item_default.value 0 _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine.ls_number_parameters.
_item_description.description ; The number of parameters refined in the least-squares process. If possible this number should include some contribution from the restrained parameters.The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least- squares restraints often depend on geometry or energy consider- ations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. ; _item.name '_refine.ls_number_parameters' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_parameters' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine.ls_number_reflns_all.
_item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. ; _item.name '_refine.ls_number_reflns_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine.ls_number_reflns_obs.
_item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low, that were flagged as observed (see _reflns.observed_criterion), and that were included in the refinement. ; _item.name '_refine.ls_number_reflns_obs' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_reflns' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine.ls_number_restraints.
_item_description.description ; The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Often restrained parameters involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site_refinement_flags. A general description of refinement constraints may appear in _refine.details. ; _item.name '_refine.ls_number_restraints' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_restraints' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_item_description.description ; Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. R = [sum||F~m~|-|F~c~|| / sum|F~m~|]; F~m~ and F~c~ are the measured and calculated structure factors. This is the conventional R factor. ; _item.name '_refine.ls_R_factor_all' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_factor_all' _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_wR_factor_all' 'alternate' _item_type.code float
_item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low, that were flagged as observed (see _reflns.observed_criterion), and that were included in the refinement. R = [sum||F~m~|-|F~c~|| / sum|F~m~|] F~m~ and F~c~ are the measured and calculated structure factors. This is the conventional R factor. ; _item.name '_refine.ls_R_factor_obs' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_factor_obs' _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_wR_factor_obs' 'alternate' _item_type.code float
save_refine.ls_R_factor_R_free.
_item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low, that were flagged as observed (see _reflns.observed_criterion), but that were excluded from refinement (see _reflns.R_free_details) so as to be included in the calculation of a "free" R-factor. R = [sum||F~m~|-|F~c~|| / sum|F~m~|] F~m~ and F~c~ are the measured and calculated structure factors. This is the conventional R factor. ; _item.name '_refine.ls_R_factor_R_free' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_wR_factor_R_free' 'alternate' _item_type.code float
save_refine.ls_restrained_S_all.
_item_description.description ; The least-squares goodness-of-fit parameter S' for all reflection data, after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. S' = {[sum(w|Ym-Yc|^2^) + sumr(wr|Pc-Pt|^2^)] / (Nref+Nrestr-Nparam)}^1/2^ where the sum is over the specified reflection data; sumr is over the restraint data; Nref is the number of reflections used in the refinement (see _refine.ls_number_reflns); Nparam is the number of refined parameters (see _refine.ls_number_parameters); Nrestr is the number of restraints (see _refine.ls_number_restraints); Ym and Yc are the measured and calculated coefficients specified in _refine.ls_structure_factor_coef; Pc and Pt are the calculated and target restraint values; w is the least-squares reflection weight [1/(e.s.d. squared)] and wr is the restraint weight. See also the definition of _refine.ls_goodness_of_fit_all. ; _item.name '_refine.ls_restrained_S_all' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_restrained_S_all' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_refine.ls_restrained_S_obs.
_item_description.description ; The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see _reflns_observed_criterion) after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. S' = {[sum(w|Ym-Yc|^2^) + sumr(wr|Pc-Pt|^2^)] / (Nref+Nrestr-Nparam)}^1/2^ where the sum is over the specified reflection data; sumr is over the restraint data; Nref is the number of reflections used in the refinement (see _refine.ls_number_reflns); Nparam is the number of refined parameters (see _refine.ls_number_parameters); Nrestr is the number of restraints (see _refine.ls_number_restraints); Ym and Yc are the measured and calculated coefficients specified in _refine.ls_structure_factor_coef; Pc and Pt are the calculated and target restraint values; w is the least-squares reflection weight [1/(e.s.d. squared)] and wr is the restraint weight. See also the definition of _refine.ls_goodness_of_fit_obs. ; _item.name '_refine.ls_restrained_S_obs' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_restrained_S_obs' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description ; The largest ratio of the final least-squares parameter shift divided by the final estimated standard deviation ; _item.name '_refine.ls_shift/esd_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_shift/esd_max' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_refine.ls_shift/esd_mean.
_item_description.description ; The average ratio of the final least-squares parameter shift divided by the final estimated standard deviation ; _item.name '_refine.ls_shift/esd_mean' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_shift/esd_mean' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_refine.ls_structure_factor_coef.
_item_description.description ; Structure-factor coefficient |F|, F^2^ or I, used in the least- squares refinement process. ; _item.name '_refine.ls_structure_factor_coef' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_structure_factor_coef' _item_default.value F _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail Inet 'net intensity' Fsqd 'structure factor squared' F 'structure factor magnitude'
save_refine.ls_weighting_details.
_item_description.description ; A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of _refine.ls_weighting_scheme is specified as 'calc'. ; _item.name '_refine.ls_weighting_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. ;
save_refine.ls_weighting_scheme.
_item_description.description ; The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight. ; _item.name '_refine.ls_weighting_scheme' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_weighting_scheme' _item_default.value sigma _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail sigma "based on measured e.s.d.'s" unit 'unit or no weights applied' calc 'calculated weights applied'
_item_description.description ; Weighted residual factor wR for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^ Y~m~ and Y~c~ are the measured and calculated coefficients specified by _refine.ls_structure_factor_coef and w is the least squares weight. ; _item.name '_refine.ls_wR_factor_all' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_wR_factor_all' _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_R_factor_all' _item_type.code float
_item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low, that were flagged as observed (see _reflns.observed_criterion), and that were included in the refinement. wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^ Y~m~ and Y~c~ are the measured and calculated coefficients specified by _refine.ls_structure_factor_coef and w is the least squares weight. ; _item.name '_refine.ls_wR_factor_obs' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_wR_factor_obs' _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_R_factor_obs' 'alternate' _item_type.code float
save_refine.ls_wR_factor_R_free.
_item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low, that were flagged as observed (see _reflns.observed_criterion), but that were excluded from refinement (see _reflns.R_free_details) so as to be included in the calculation of a "free" R-factor. wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^ Y~m~ and Y~c~ are the measured and calculated coefficients specified by _refine.ls_structure_factor_coef and w is the least squares weight. ; _item.name '_refine.ls_wR_factor_R_free' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_R_factor_R_free' 'alternate' _item_type.code float
_item_description.description ; The maximum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_max' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1.0 _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
_item_description.description ; The minimum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_min' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1.0 _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
_category.description ; Data items in the REFINE_B_ISO category record details about the treatment of isotropic B (temperature) factors during refinement. ; _category.id _category.id _category.mandatory_code no _category_key.name '_refine_b_iso.class' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _refine_b_iso.class _refine_b_iso.treatment 'protein' isotropic 'solvent' isotropic 'inhibitor' isotropic ;
_item_description.description ; A class of atoms treated similarly for isotropic B (temperature) factor refinement. ; _item.name '_refine_b_iso.class' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'all' 'protein' 'solvent' 'sugar-phosphate backbone'
_item_description.description ; A description of special aspects of the isotropic B (temperature) factor refinement for the class of atoms described in _refine_b_iso.class. ; _item.name '_refine_b_iso.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The temperature factors of atoms in the side chain of Arg 92 were held fixed due to unstable behavior in refinement. ;
_item_description.description ; The treatment of isotropic B (temperature) factor refinement for a class of atoms defined in _refine_b_iso.class. ; _item.name '_refine_b_iso.treatment' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value fixed isotropic anisotropic
_item_description.description ; The value of the isotropic B (temperature) factor assigned to a class of atoms defined in _refine_b_iso.class. Meaningful only for atoms with fixed isotropic B (temperature) factors. ; _item.name '_refine_b_iso.value' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'angstroms_squared'
_category.description ; Data items in the REFINE category record details about the various steps along the way in the refinement of the structure. These data items are not meant to be as thorough as description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics. ; _category.id _category.id _category.mandatory_code no _category_key.name '_refine_hist.cycle_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
_item_description.description ; The value of refine_hist.cycle_id must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_refine_hist.cycle_id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
_item_description.description ; The highest resolution for the interplanar spacing in the reflection data for this cycle of refinement. ; _item.name '_refine_hist.d_res_high' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; The lowest resolution for the interplanar spacing in the reflection data for this cycle of refinement. ; _item.name '_refine_hist.d_res_low' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Description of special aspects of this cycle of the refinement process. ; _item.name '_refine_hist.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Residues 13-17 fit and added to model; substantinal rebuilding of loop containing residues 43-48; addition of first atoms to solvent model; ten cycles of Prolsq refinement. ;
save_refine_hist.number_atoms_solvent.
_item_description.description ; The number of solvent atoms that were included in the model at this cycle of the refinement. ; _item.name '_refine_hist.number_atoms_solvent' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine_hist.number_atoms_total.
_item_description.description ; The total number of atoms that were included in the model at this cycle of the refinement. ; _item.name '_refine_hist.number_atoms_total' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine_hist.number_reflns_obs.
_item_description.description ; The number of reflections that were included in this cycle of the refinement. ; _item.name '_refine_hist.number_reflns_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine_hist.R_factor_obs.
_item_description.description ; Residual factor R for reflections that were included in the this cycle of the refinement. R = [sum||F~m~|-|F~c~|| / sum|F~m~|] F~m~ and F~c~ are the measured and calculated structure factors. This is the conventional R factor. ; _item.name '_refine_hist.R_factor_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_refine_ls.number_reflns_R_free.
_item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low, that were flagged as observed (see _reflns.observed_criterion), but that were excluded from refinement (see _reflns.R_free_details) so as to be included in the calculation of a "free" R-factor. ; _item.name '_refine_ls.number_reflns_R_free' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_category.description ; Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during least-squares refinement. ; _category.id _category.id _category.mandatory_code no _category_key.name '_refine_ls_restr.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal_target _refine_ls_restr.dev_ideal _refine_ls_restr.number _refine_ls_restr.criterion _refine_ls_restr.rejects 'bond_d' 0.020 0.018 1654 '> 2\s' 22 'angle_d' 0.030 0.038 2246 '> 2\s' 139 'planar_d' 0.040 0.043 498 '> 2\s' 21 'planar' 0.020 0.015 270 '> 2\s' 1 'chiral' 0.150 0.177 278 '> 2\s' 2 'singtor_nbd' 0.500 0.216 582 '> 2\s' 0 'multtor_nbd' 0.500 0.207 419 '> 2\s' 0 'xyhbond_nbd' 0.500 0.245 149 '> 2\s' 0 'planar_tor' 3.0 2.6 203 '> 2\s' 9 'staggered_tor' 15.0 17.4 298 '> 2\s' 31 'orthonormal_tor' 20.0 18.1 12 '> 2\s' 1 ;
save_refine_ls_restr.criterion.
_item_description.description ; A criterion used to define a parameter value that deviates significantly from its ideal value in the model obtained by restrained least-squares refinement. ; _item.name '_refine_ls_restr.criterion' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case '> 3\s'
save_refine_ls_restr.dev_ideal.
_item_description.description ; For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 \%A (rms) from ideal values in current model. ; _item.name '_refine_ls_restr.dev_ideal' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_refine_ls_restr.dev_ideal_target.
_item_description.description ; For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. ; _item.name '_refine_ls_restr.dev_ideal_target' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description ; The number parameters of this type subjected to restraint in least-squares refinement. ; _item.name '_refine_ls_restr.number' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_item_description.description ; The number of parameters of this type that deviate from ideal values by more than the amount defined in _refine_ls_restr.criterion in the model obtained by restrained least-squares refinement. ; _item.name '_refine_ls_restr.rejects' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_item_description.description ; The type of the parameter being restrained. An explicit set of data values are provided for programs Protin/ Prolsq (beginning with p_) and X-plor (beginning with x_). As computer programs will evolve, these data values are given as examples, and not as an enumeration list. Computer programs converting a CIF to a refinement table will expect the exact form of the data values given here to be used. ; _item.name '_refine_ls_restr.type' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case _item_examples.detail 'p_bond_d' 'bond distance' 'p_angle_d' 'bond angle expressed as a distance' 'p_planar_d' 'planar 1,4 distance' 'p_xhbond_d' 'x-h bond distance' 'p_xhangle_d' 'x-h bond angle expressed as a distance' 'p_hydrog_d' 'hydrogen distance' 'p_special_d' 'special distance' 'p_planar' 'planes' 'p_chiral' 'chiral centers' 'p_singtor_nbd' 'single-torsion non-bonded contact' 'p_multtor_nbd' 'multiple-torsion non-bonded contact' 'p_xyhbond_nbd' 'possible (x....y) hydrogen-bond' 'p_xhyhbond_nbd' 'possible (x-h..y) hydrogen-bond' 'p_special_tor' 'special torsion angle' 'p_planar_tor' 'planar torsion angle' 'p_staggered_tor' 'staggered torsion angle' 'p_orthonormal_tor' 'orthonormal torsion angle' 'p_mcbond_it' 'main-chain bond isotropic thermal factor' 'p_mcangle_it' 'main-chain angle isotropic thermal factor' 'p_scbond_it' 'side-chain bond isotropic thermal factor' 'p_scangle_it' 'side-chain angle isotropic thermal factor' 'p_xhbond_it' 'x-h bond isotropic thermal factor' 'p_xhangle_it' 'x-h angle isotropic thermal factor' 'p_special_it' 'special isotropic thermal factor'
_category.description ; Data items in the REFINE_LS_SHELL category record details about the results of least-squares refinement, broken out by shells of resolution. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_refine_ls_shell.d_res_low' '_refine_ls_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _refine_ls_shell.d_res_low _refine_ls_shell.d_res_high _refine_ls_shell.reflns _refine_ls_shell.R_factor_obs 8.00 4.51 1226 0.196 4.51 3.48 1679 0.146 3.48 2.94 2014 0.160 2.94 2.59 2147 0.182 2.59 2.34 2127 0.193 2.34 2.15 2061 0.203 2.15 2.00 1647 0.188 ;
save_refine_ls_shell.d_res_high.
_item_description.description ; The highest resolution for the interplanar spacing in the reflection data in this shell. These is the largest d value. ; _item.name '_refine_ls_shell.d_res_high' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_refine_ls_shell.d_res_low.
_item_description.description ; The lowest resolution for the interplanar spacing in the reflection data in this shell. This is the smallest d value. ; _item.name '_refine_ls_shell.d_res_low' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_refine_ls_shell.number_reflns_all.
_item_description.description ; The total number of reflections in this shell. ; _item.name '_refine_ls_shell.number_reflns_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine_ls_shell.number_reflns_obs.
_item_description.description ; The number of reflections in this shell that were flagged as observed (see _reflns.observed_criterion) and included in the refinement. ; _item.name '_refine_ls_shell.number_reflns_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine_ls_shell.number_reflns_R_free.
_item_description.description ; The number of reflections in this shell that were flagged as observed (see _reflns.observed_criterion) but excluded from refinement (see _reflns.R_free_details) so as to be included in the calculation of a "free" R-factor. ; _item.name '_refine_ls_shell.number_reflns_R_free' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine_ls_shell.R_factor_all.
_item_description.description ; Residual factor R for all reflections in this shell. R = [sum||F~m~|-|F~c~|| / sum|F~m~|]; F~m~ and F~c~ are the measured and calculated structure factors. This is the conventional R factor. ; _item.name '_refine_ls_shell.R_factor_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.wR_factor_all' 'alternate' _item_type.code float
save_refine_ls_shell.R_factor_obs.
_item_description.description ; Residual factor R for reflections in this shell that were flagged as observed (see _reflns.observed_criterion) and included in the refinement. R = [sum||F~m~|-|F~c~|| / sum|F~m~|] F~m~ and F~c~ are the measured and calculated structure factors. This is the conventional R factor. ; _item.name '_refine_ls_shell.R_factor_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.wR_factor_obs' 'alternate' _item_type.code float
save_refine_ls_shell.R_factor_R_free.
_item_description.description ; Residual factor R for reflections in this shell that were flagged as observed (see _reflns.observed_criterion) but excluded from refinement (see _reflns.R_free_details) so as to be included in the calculation of a "free" R-factor. R = [sum||F~m~|-|F~c~|| / sum|F~m~|] F~m~ and F~c~ are the measured and calculated structure factors. This is the conventional R factor. ; _item.name '_refine_ls_shell.R_factor_R_free' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.wR_factor_R_free' 'alternate' _item_type.code float
save_refine_ls_shell.wR_factor_all.
_item_description.description ; Weighted residual factor wR for all reflections in this shell. wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^ Y~m~ and Y~c~ are the measured and calculated coefficients specified by _refine.ls_structure_factor_coef and w is the least squares weight. ; _item.name '_refine_ls_shell.wR_factor_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.R_factor_all' 'alternate' _item_type.code float
save_refine_ls_shell.wR_factor_obs.
_item_description.description ; Weighted residual factor wR for reflections in this shell that were flagged as observed (see _reflns.observed_criterion) and included in the refinement. wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^ Y~m~ and Y~c~ are the measured and calculated coefficients specified by _refine.ls_structure_factor_coef and w is the least squares weight. ; _item.name '_refine_ls_shell.wR_factor_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.R_factor_obs' 'alternate' _item_type.code float
save_refine_ls_shell.wR_factor_R_free.
_item_description.description ; Weighted residual factor wR for reflections in this shell that were flagged as observed (see _reflns.observed_criterion) but excluded from refinement (see _reflns.R_free_details) so as to be included in the calculation of a "free" R-factor. wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^ Y~m~ and Y~c~ are the measured and calculated coefficients specified by _refine.ls_structure_factor_coef and w is the least squares weight. ; _item.name '_refine_ls_shell.wR_factor_R_free' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.R_factor_R_free' 'alternate' _item_type.code float
_category.description ; Data items in the REFINE_OCCUPANCY category record details about the treatment of atomic occupancies during refinement. ; _category.id _category.id _category.mandatory_code no _category_key.name '_refine_occupancy.class' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.value _refine_occupancy.details 'protein' fix 1.00 . 'solvent' fix 1.00 . 'inhibitor orientation 1' fix 0.65 . 'inhibitor orientation 2' fix 0.35 ; The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. ; ;
_item_description.description ; The class of atoms treated similarly for occupancy refinement. ; _item.name '_refine_occupancy.class' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'all' 'protein' 'solvent' 'sugar-phosphate backbone'
save_refine_occupancy.details.
_item_description.description ; A description of special aspects of the occupancy refinement for a class of atoms described in _refine_occupancy.class. ; _item.name '_refine_occupancy.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. ;
save_refine_occupancy.treatment.
_item_description.description ; The treatment of occupancy refinement for a class of atoms described in _refine_occupancy.class. ; _item.name '_refine_occupancy.treatment' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail fix fixed ref refined
_item_description.description ; The value of occupancy assigned to a class of atoms defined in _refine_occupancy.class. Meaningful only for atoms with fixed occupancy. ; _item.name '_refine_occupancy.value' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float loop_ _item_examples.case 1.0 0.41
_category.description ; Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in loop lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_refln.index_h' '_refln.index_k' '_refln.index_l' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ; ; Example 2 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [(1993). Acta Cryst. C49, 1352-1354]. ; ; loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_squared_calc _refln.F_squared_meas _refln.F_squared_sigma _refln.observed_status 2 0 0 85.57 58.90 1.45 o 3 0 0 15718.18 15631.06 30.40 o 4 0 0 55613.11 49840.09 61.86 o 5 0 0 246.85 241.86 10.02 o 6 0 0 82.16 69.97 1.93 o 7 0 0 1133.62 947.79 11.78 o 8 0 0 2558.04 2453.33 20.44 o 9 0 0 283.88 393.66 7.79 o 10 0 0 283.70 171.98 4.26 o ;
_item_description.description ; The calculated value of structure-factor component A in electrons. A = |F|cos(phase) ; _item.name '_refln.A_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_A_calc' _item_type.code float _item_units.code 'electrons'
_item_description.description ; The measured value of structure-factor component A in electrons. A = |F|cos(phase) ; _item.name '_refln.A_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_A_meas' _item_type.code float _item_units.code 'electrons'
_item_description.description ; The calculated value of structure-factor component B in electrons. B = |F|sin(phase) ; _item.name '_refln.B_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_B_calc' _item_type.code float _item_units.code 'electrons'
_item_description.description ; The measured value of structure-factor component B in electrons. B = |F|sin(phase) ; _item.name '_refln.B_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_B_meas' _item_type.code float _item_units.code 'electrons'
_item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item_aliases.alias_name '_refln_crystal_id'
_item_description.description ; The calculated value of the structure factor, in electrons. ; _item.name '_refln.F_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_calc' _item_type.code float _item_units.code 'electrons'
_item_description.description ; The measured value of the structure factor, in electrons. ; _item.name '_refln.F_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_meas' _item_type.code float _item_units.code 'electrons'
_item_description.description ; The standard deviation (derived from measured value) of the structure factor, in electrons. ; _item.name '_refln.F_sigma' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_sigma' _item_type.code float _item_units.code 'electrons'
_item_description.description ; The calculated value of the squared structure factor, in electrons squared. ; _item.name '_refln.F_squared_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_calc' _item_type.code float _item_units.code 'electrons_squared'
_item_description.description ; The measured value of the squared structure factor, in electrons squared. ; _item.name '_refln.F_squared_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_meas' _item_type.code float _item_units.code 'electrons_squared'
_item_description.description ; The estimated standard deviation of the squared structure factor, in electrons squared. ; _item.name '_refln.F_squared_sigma' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_sigma' _item_type.code float _item_units.code 'electrons_squared'
_item_description.description ; For phasing experiments using MIR, the Hendrickson-Lattman coefficient A. A = please fill in Eleanor where... ; _item.name '_refln.HL_coeff_A' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description ; Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_refln_index_h' loop_ _item_dependent.dependent_name '_refln.index_k' '_refln.index_l' _item_type.code int
_item_description.description ; Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_refln_index_k' loop_ _item_dependent.dependent_name '_refln.index_h' '_refln.index_l' _item_type.code int
_item_description.description ; Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' _item_aliases.alias_name '_refln_index_l' loop_ _item_dependent.dependent_name '_refln.index_h' '_refln.index_k' _item_type.code int
_item_description.description ; The calculated value of the intensity, in the measured units. ; _item.name '_refln.intensity_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_calc' _item_type.code float
_item_description.description ; The measured value of the intensity, in the measured units. ; _item.name '_refln.intensity_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_meas' _item_type.code float
_item_description.description ; The standard deviation (derived from measured data) of the intensity, in the measured units. ; _item.name '_refln.intensity_sigma' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_sigma' _item_type.code float
save_refln.mean_path_length_tbar.
_item_description.description ; Mean path length through the crystal for this reflection. ; _item.name '_refln.mean_path_length_tbar' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_mean_path_length_tbar' _item_type.code float _item_units.code 'millimetres'
_item_description.description ; The calculated value of the structure-factor phase in degrees. ; _item.name '_refln.phase_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_phase_calc' _item_type.code float _item_units.code 'degrees'
_item_description.description ; The measured value of the structure-factor phase in degrees. ; _item.name '_refln.phase_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_phase_meas' _item_type.code float _item_units.code 'degrees'
_item_description.description ; Status of reflection in the structure refinement process. ; _item.name '_refln.refinement_status' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_refinement_status' _item_default.value incl _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail incl 'included in ls process' excl 'excluded from ls process' extn 'excluded due to extinction'
_item_description.description ; The (sin theta)/lambda for this reflection. ; _item.name '_refln.sint/lambda' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_sint/lambda' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'reciprocal_angstroms'
_item_description.description ; Classification of a reflection so at to indicate its status with respect to inclusion in refinement and calculation of R-factors. ; _item.name '_refln.status' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_observed_status' _item_default.value o _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail o ; satisfies _refine.d_res_high satisfies _refine.d_res_low observed by _reflns_observed_criterion ; < ; satisfies _refine.d_res_high satisfies _refine.d_res_low unobserved by _reflns_observed_criterion ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine.d_res_high' l 'does not satifsy _refine.d_res_low' f ; satisfies _refine.d_res_high satisfies _refine.d_res_low observed by _reflns_observed_criterion excluded from refinement so as to be included in calculation of "free" R-factor ;
_item_description.description ; The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. ; _item.name '_refln.symmetry_epsilon' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_symmetry_epsilon' _item_range.maximum 32 _item_range.minimum 1 _item_type.code int
save_refln.symmetry_multiplicity.
_item_description.description ; The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor value because of the space-group symmetry and the Friedel relationship. ; _item.name '_refln.symmetry_multiplicity' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_symmetry_multiplicity' _item_range.maximum 24 _item_range.minimum 1 _item_type.code int
_item_description.description ; The mean wavelength of radiation used to measure this reflection. This is an important parameter for data collected using energy- dispersive detectors or the Laue method. ; _item.name '_refln.wavelength' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_wavelength' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category. ; _item_aliases.alias_name '_refln_wavelength_id'
_category.description ; Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; _category.id _category.id _category.mandatory_code no _category_key.name '_reflns.block_id' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _reflns.data_reduction_method ; Xengen program scalei. Anomalous paris were merged. Scaling proceeded in several passes, beginning with 1-parameter fit and ending with 3-parameter fit. ; _reflns.data_reduction_details ; Merging and scaling based on only those reflections with I > \s(I). ; _reflns.d_resolution_high 2.00 _reflns.d_resolution_low 8.00 _reflns.limit_h_max 22 _reflns.limit_h_min 0 _reflns.limit_k_max 46 _reflns.limit_k_min 0 _reflns.limit_l_max 57 _reflns.limit_l_min 0 _reflns.number_obs 7228 _reflns.observed_criterion '> 1 \s(I)' _reflns.details none ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _reflns.limit_h_min 0 _reflns.limit_h_max 6 _reflns.limit_k_min 0 _reflns.limit_k_max 17 _reflns.limit_l_min 0 _reflns.limit_l_max 22 _reflns.number_all 1592 _reflns.number_obs 1408 _reflns.observed_criterion F_>_6.0_\s(F) _reflns.d_resolution_high 0.8733 _reflns.d_resolution_low 11.9202 ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_reflns.d_resolution_high.
_item_description.description ; The highest resolution for the interplanar spacings in the reflection data. This is the smallest d value. ; _item.name '_reflns.d_resolution_high' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_d_resolution_high' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; The lowest resolution for the interplanar spacings in the reflection data. This is the largest d value. ; _item.name '_reflns.d_resolution_low' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_d_resolution_low' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_reflns.data_reduction_details.
_item_description.description ; A description of special aspects of the data reduction procedures. ; _item.name '_reflns.data_reduction_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Merging and scaling based on only those reflections with I > sig(I). ;
save_reflns.data_reduction_method.
_item_description.description ; The method used in reducing the data. Note that this is not the computer program used, which is described in _computing.save_reduction. Rather this data item should be used to describe significant methodological options used within the data reduction programs. ; _item.name '_reflns.data_reduction_method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Profile fitting by methods of Kabsch (19xx). Scaling used spherical harmonic coefficients. ;
_item_description.description ; A description of reflection data not covered by the other data names. It should include details of the Friedel reflection data. ; _item.name '_reflns.details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_special_details' _item_type.code char
_item_description.description ; Maximum value of Miller index h for the reflection data. This need not be have the same value as _diffrn_reflns.limit_h_max. ; _item.name '_reflns.limit_h_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_h_max' _item_type.code int
_item_description.description ; Minimum value of Miller index h for the reflection data. This need not be have the same value as _diffrn_reflns.limit_h_min. ; _item.name '_reflns.limit_h_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_h_min' _item_type.code int
_item_description.description ; Maximum value of Miller index k for the reflection data. This need not be have the same value as _diffrn_reflns.limit_k_max. ; _item.name '_reflns.limit_k_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_k_max' _item_type.code int
_item_description.description ; Minimum value of Miller index k for the reflection data. This need not be have the same value as _diffrn_reflns.limit_k_min. ; _item.name '_reflns.limit_k_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_k_min' _item_type.code int
_item_description.description ; Maximum value of Miller index l for the reflection data. This need not be have the same value as _diffrn_reflns.limit_l_max. ; _item.name '_reflns.limit_l_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_l_max' _item_type.code int
_item_description.description ; Minimum value of Miller index l for the reflection data. This need not be have the same value as _diffrn_reflns.limit_l_min. ; _item.name '_reflns.limit_l_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_l_min' _item_type.code int
_item_description.description ; The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel equivalent reflections according to the nature of the structure and the procedures used. The item _reflns.details describes the reflection data. ; _item.name '_reflns.number_all' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_number_total' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_item_description.description ; The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see _reflns_observed_criterion). This number may contain Friedel equivalent reflections according to the nature of the structure and the procedures used. ; _item.name '_reflns.number_obs' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_number_observed' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_reflns.observed_criterion.
_item_description.description ; The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of an e.s.d. threshold. ; _item.name '_reflns.observed_criterion' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_observed_criterion' _item_type.code char _item_examples.case '>2sigma(I)'
_item_description.description ; A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a "free" R-factor. ; _item.name '_reflns.R_free_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The data set was sorted with l varying most rapidly and h varying least rapidly. Every 10th reflection is this sorted list was excluded from refinement and included in the calculation of a "free" R-factor. ;
_category.description ; Data items in the REFLNS_SCALE category record details about the structure factor scales. They are referenced from within the REFLN list through _refln.scale_group_code. ; _category.id _category.id _category.mandatory_code no _category_key.name '_reflns_scale.group_code' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ;
_item_description.description ; The code identifying a scale _reflns_scale.meas_. These are linked to the REFLN list by the _refln.scale_group_code. ; loop_ _item.name _item.category_id _item.mandatory_code '_reflns_scale.group_code' reflns_scale yes '_refln.scale_group_code' refln yes _item_aliases.alias_name '_reflns_scale_group_code' loop_ _item_linked.child_name _item_linked.parent_name '_refln.scale_group_code' '_reflns_scale.group_code' _item_type.code char loop_ _item_examples.case 1 2 3 s1 A B c1 c2 c3
_item_description.description ; The code identifying a scale _reflns_scale.meas_. These are linked to the REFLN list by the _refln.scale_group_code. ; loop_ _item.name _item.category_id _item.mandatory_code '_reflns_scale.group_code' reflns_scale yes '_refln.scale_group_code' refln yes _item_aliases.alias_name '_reflns_scale_group_code' loop_ _item_linked.child_name _item_linked.parent_name '_refln.scale_group_code' '_reflns_scale.group_code' _item_type.code char loop_ _item_examples.case 1 2 3 s1 A B c1 c2 c3
_item_description.description ; A scale associated with _reflns_scale.group_code. These codes may not correspond to those in the DIFFRN_SCALE list. ; _item.name '_reflns_scale.meas_F' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_F' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_reflns_scale.meas_F_squared.
_item_description.description ; A scale associated with _reflns_scale.group_code. These codes may not correspond to those in the DIFFRN_SCALE list. ; _item.name '_reflns_scale.meas_F_squared' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_F_squared' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_reflns_scale.meas_intensity.
_item_description.description ; A scale associated with _reflns_scale.group_code. These codes may not correspond to those in the DIFFRN_SCALE list. ; _item.name '_reflns_scale.meas_intensity' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_intensity' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_category.description ; Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items, as broken down by shells of resolution. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_reflns_shell.d_res_high' '_reflns_shell.d_res_low' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI/sigI_obs _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.possible_%_obs _reflns_shell.Rmerge_F_obs 31.38 3.82 69.8 9024 2540 96.8 1.98 3.82 3.03 26.1 7413 2364 95.1 3.85 3.03 2.65 10.5 5640 2123 86.2 6.37 2.65 2.41 6.4 4322 1882 76.8 8.01 2.41 2.23 4.3 3247 1714 70.4 9.86 2.23 2.10 3.1 1140 812 33.3 13.99 ;
_item_description.description ; The highest for the interplanar spacing in the reflection data in this shell. This is the smallest d value. ; _item.name '_reflns_shell.d_res_high' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description ; The lowest resolution for the interplanar spacing in the reflection data in this shell. This is the largest d value. ; _item.name '_reflns_shell.d_res_low' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_reflns_shell.meanI/sigI_all.
_item_description.description ; The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard deviations of the intensities of all reflections in the resolution shell. ; _item.name '_reflns_shell.meanI/sigI_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_reflns_shell.meanI/sigI_obs.
_item_description.description ; The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns_observed_criterion) in this shell to the mean of the standard deviations of the intensities of the 'observed' reflections in the resolution shell. . ; _item.name '_reflns_shell.meanI/sigI_obs' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_reflns_shell.number_measured_all.
_item_description.description ; The total number of diffraction reflections measured for this resolution shell. ; _item.name '_reflns_shell.number_measured_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_reflns_shell.number_measured_obs.
_item_description.description ; The number of diffraction reflections classified as 'observed' (see _reflns_observed_criterion) measured for this resolution shell ; _item.name '_reflns_shell.number_measured_obs' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_reflns_shell.number_possible.
_item_description.description ; The number of unique reflections it is possible to measure in this reflection shell. ; _item.name '_reflns_shell.number_possible' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code int
save_reflns_shell.number_unique_all.
_item_description.description ; The total number of diffraction reflections which are symmetrically unique after merging for this resolution shell. ; _item.name '_reflns_shell.number_unique_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_reflns_shell.number_unique_obs.
_item_description.description ; The total number of diffraction reflections classified as 'observed' (see _reflns_observed_criterion) which are symmetrically unique after merging for this resolution shell. ; _item.name '_reflns_shell.number_unique_obs' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_reflns_shell.percent_possible_all.
_item_description.description ; The percentage of geometrically possible diffraction reflections represented by all diffraction reflections measured for this resolution shell. ; _item.name '_reflns_shell.percent_possible_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_reflns_shell.percent_possible_obs.
_item_description.description ; The percentage of geometrically possible diffraction reflections represented by diffraction reflections classified as 'observed' (see _reflns_observed_criterion) measured for this resolution shell. ; _item.name '_reflns_shell.percent_possible_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_reflns_shell.Rmerge_F_all.
_item_description.description ; The value of Rmerge(F) for all reflections in a given shell. Rmerge(F) = sum~i~ [sum~j~ |F~j~-|] / sum~i~ [sum~j~ | |] were sum~i is taken over all reflections and sum~j is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_F_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_reflns_shell.Rmerge_F_obs.
_item_description.description ; The value of Rmerge(F) for reflections classified as 'observed' (see _reflns_observed_criterion) in a given shell. Rmerge(F) = sum~i~ [sum~j~ |F~j~-|] / sum~i~ [sum~j~ | |] were sum~i is taken over all reflections and sum~j is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_F_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_reflns_shell.Rmerge_I_all.
_item_description.description ; The value of Rmerge(I) for all reflections in a given shell. Rmerge(I) - sum~i~ [sum~j~ |I~j~-|] / sum~i~ [sum~j~ ||] were sum~i is taken over all reflections and sum~j is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_I_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
save_reflns_shell.Rmerge_I_obs.
_item_description.description ; The value of Rmerge(I) for reflections classified as 'observed' (see _reflns_observed_criterion) in a given shell. Rmerge(I) - sum~i~ [sum~j~ |I~j~-|] / sum~i~ [sum~j~ ||] were sum~i is taken over all reflections and sum~j is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_I_obs' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_category.description ; Data items in the STRUCT category record details about the description of the crystallographic structure. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct.block_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _struct.title ; HIV-1 protease complex with acetyl-pepstatin ; loop_ _struct.keywords 'enzyme-inhibitor complex' 'aspartyl protease' 'structure-based drug design' 'static disorder' ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; Keywords for the structure archived in the CIF. ; _item.name '_struct.keywords' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'serine protease' 'inhibited complex' 'high resolution refinement'
_item_description.description ; A title for the CIF. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. ; _item.name '_struct.title' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case "5'-D(*(I)CP*CP*GP*G)-3" 'T4 lysozyme mutant - S32A' 'hen egg white lysozyme at -30 degrees C' 'quail egg white lysozyme at 2 atmospheres'
_category.description ; Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_asym.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_asym.id _struct_asym.entity_id _struct_asym.details A 1 'one monomer of the dimeric enzyme' B 1 'one monomer of the dimeric enzyme' C 2 'one partially occupied position for the inhibitor' D 2 'one partially occupied position for the inhibitor' ;
_item_description.description ; A description of special aspects of this portion of the contents of the asymmetric unit. ; _item.name '_struct_asym.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative id 2 should be used with this biological unit. ;
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; The value of _struct_asym.id must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_asym.id' struct_asym yes '_atom_site.label_asym_id' atom_site yes '_struct_biol_gen.asym_id' struct_biol_gen yes '_struct_conf.beg_label_asym_id' struct_conf yes '_struct_conf.end_label_asym_id' struct_conf yes '_struct_conn.ptnr1_label_asym_id' struct_conn yes '_struct_conn.ptnr2_label_asym_id' struct_conn yes '_struct_mon_nucl.label_asym_id' struct_mon_nucl yes '_struct_mon_prot.label_asym_id' struct_mon_prot yes '_struct_mon_prot_cis.label_asym_id' struct_mon_prot_cis yes '_struct_ncs_dom_gen.beg_label_asym_id' struct_ncs_dom_gen yes '_struct_ncs_dom_gen.end_label_asym_id' struct_ncs_dom_gen yes '_struct_site_gen.label_asym_id' struct_site yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_asym_id' '_struct_asym.id' '_struct_biol_gen.asym_id' '_struct_asym.id' '_struct_conf.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_conf.end_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr1_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr2_label_asym_id' '_atom_site.label_asym_id' '_struct_mon_nucl.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot_cis.label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_gen.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_gen.end_label_asym_id' '_atom_site.label_asym_id' '_struct_site_gen.label_asym_id' '_atom_site.label_asym_id' _item_type.code char loop_ _item_examples.case 1 A 2B3
_item_description.description ; The value of _struct_asym.id must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_asym.id' struct_asym yes '_atom_site.label_asym_id' atom_site yes '_struct_biol_gen.asym_id' struct_biol_gen yes '_struct_conf.beg_label_asym_id' struct_conf yes '_struct_conf.end_label_asym_id' struct_conf yes '_struct_conn.ptnr1_label_asym_id' struct_conn yes '_struct_conn.ptnr2_label_asym_id' struct_conn yes '_struct_mon_nucl.label_asym_id' struct_mon_nucl yes '_struct_mon_prot.label_asym_id' struct_mon_prot yes '_struct_mon_prot_cis.label_asym_id' struct_mon_prot_cis yes '_struct_ncs_dom_gen.beg_label_asym_id' struct_ncs_dom_gen yes '_struct_ncs_dom_gen.end_label_asym_id' struct_ncs_dom_gen yes '_struct_site_gen.label_asym_id' struct_site yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_asym_id' '_struct_asym.id' '_struct_biol_gen.asym_id' '_struct_asym.id' '_struct_conf.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_conf.end_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr1_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr2_label_asym_id' '_atom_site.label_asym_id' '_struct_mon_nucl.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot_cis.label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_gen.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_gen.end_label_asym_id' '_atom_site.label_asym_id' '_struct_site_gen.label_asym_id' '_atom_site.label_asym_id' _item_type.code char loop_ _item_examples.case 1 A 2B3
_category.description ; Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light and heavy chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_biol.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_biol.id _struct_biol.details 1 ; significant deviations from twofold symmetry exist in this dimeric enzyme ; 2 ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (2) is roughly twofold symmetric to biological unit (3). Disorder in the protein chain indicated with alternative id 1 should be used with this biological unit. ; 3 ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative id 2 should be used with this biological unit. ; ;
_item_description.description ; A description of special aspects of the biological unit. ; _item.name '_struct_biol.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative id 2 should be used with this biological unit. ;
_item_description.description ; The value of _struct_biol.id must uniquely identify a record in the STRUCT_BIOL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_biol.id' struct_biol yes '_struct_biol_gen.biol_id' struct_biol_gen yes '_struct_biol_keywords.biol_id' struct_biol_keywords yes '_struct_biol_view.biol_id' struct_biol_view yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_biol_gen.biol_id' '_struct_biol.id' '_struct_biol_keywords.biol_id' '_struct_biol.id' '_struct_biol_view.biol_id' '_struct_biol.id' _item_type.code char
_category.description ; Data items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit. The STRUCT_BIOL_GEN data items provide the specifications of the components that constitute that biological unit, which may include symmetry elements. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_biol_gen.biol_id' '_struct_biol_gen.asym_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry 1 A 1_555 1 B 1_555 2 A 1_555 2 B 1_555 2 C 1_555 3 A 1_555 3 B 1_555 3 D 1_555 ;
_item_description.description ; This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
_item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ;
_item_description.description ; A description of special aspects of the symmetry generation of this portion of the biological structure. ; _item.name '_struct_biol_gen.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. ;
save_struct_biol_gen.symmetry.
_item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_biol_gen.asym_id to generate a portion of the biological structure. ; _item.name '_struct_biol_gen.symmetry' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
_category.description ; Data items in the STRUCT_BIOL_KEYWORDS category record details about keywords that describe each biological unit. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_biol_keywords.biol_id' '_struct_biol_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_biol_keywords.biol_id _struct_biol_keywords.text 1 'aspartyl-protease' 1 'aspartic-protease' 1 'acid-protease' 1 'aspartyl-proteinase' 1 'aspartic-proteinase' 1 'acid-proteinase' 1 'enzyme' 1 'protease' 1 'proteinase' 1 'dimer' 2 'drug-enzyme complex' 2 'inhibitor-enzyme complex' 2 'drug-protease complex' 2 'inhibitor-protease complex' 3 'drug-enzyme complex' 3 'inhibitor-enzyme complex' 3 'drug-protease complex' 3 'inhibitor-protease complex' ;
save_struct_biol_keywords.biol_id.
_item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ;
save_struct_biol_keywords.text.
_item_description.description ; Keywords describing this biological entity. ; _item.name '_struct_biol_keywords.text' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case antibody antigen enzyme cytokine tRNA
_category.description ; Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate a useful didactic view of the biological structure. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_biol_view.biol_id' '_struct_biol_view.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ;
save_struct_biol_view.biol_id.
_item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ;
save_struct_biol_view.details.
_item_description.description ; A description of special aspects of this view of the biological structure. This data item can be used as a figure legend, if desired. ; _item.name '_struct_biol_view.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; The enzyme has been oriented with the molecular twofold axis aligned with the horizontal axis of the figure. ;
_item_description.description ; The value of _struct_biol_view.id must uniquely identify a record in the STRUCT_BIOL_VIEW list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_biol_view.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Figure 1' 'unliganded enzyme' 'view down enzyme active site'
save_struct_biol_view.rot_matrix.
_item_description.description ; The matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_VIEW_GEN category to a view useful for describing the structure. The conventions used in the rotation are described in _struct_site_view_details. |11 12 13| x x' |21 22 23| ( y ) Cartesian = ( y' ) reoriented Cartesian |31 32 33| z z' ; _item.name '_struct_biol_view.rot_matrix' _item.category_id _item.category_id _item.mandatory_code no _item_structure.code 'matrix3x3' _item_structure.organization 'rowwise' _item_type.code float
_category.description ; Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. The STRUCT_CONF_TYPE records define the criteria used to identify the backbone conformations. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_conf.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_conf.id _struct_conf.conf_type_id _struct_conf.beg_label_res_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.end_label_res_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.details HELX1 HELX-RHAL ARG A 87 GLN A 92 . HELX2 HELX-RHAL ARG B 287 GLN B 292 . STRN1 STRN PRO A 1 LEU A 5 . STRN2 STRN CYS B 295 PHE B 299 . STRN3 STRN CYS A 95 PHE A 299 . STRN4 STRN PRO B 201 LEU B 205 . # - - - - data truncated for brevity - - - - TURN1 TURN-TY1P ILE A 15 GLN A 18 . TURN2 TURN-TY2 GLY A 49 GLY A 52 . TURN3 TURN-TY1P ILE A 55 HIS A 69 . TURN4 TURN-TY1 THR A 91 GLY A 94 . # - - - - data truncated for brevity - - - - ;
save_struct_conf.beg_label_asym_id.
_item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_conf.beg_label_res_id.
_item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_conf.beg_label_seq_id.
_item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
_item_description.description ; A description of special aspects of the conformation assignment. ; _item.name '_struct_conf.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_struct_conf.end_label_asym_id.
_item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_conf.end_label_res_id.
_item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_conf.end_label_seq_id.
_item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
_item_description.description ; The value of _struct_conf.id must uniquely identify a record in the STRUCT_CONF list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_conf.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
_category.description ; Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_conf_type.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_conf_type.id _struct_conf_type.criteria _struct_conf_type.reference HELX-RHAL 'author judgement' . STRN 'author judgement' . TURN-TY1 'author judgement' . TURN-TY1P 'author judgement' . TURN-TY2 'author judgement' . TURN-TY2P 'author judgement' . ;
save_struct_conf_type.criteria.
_item_description.description ; The criteria used to assign this conformation type. ; _item.name '_struct_conf_type.criteria' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'author judgement' 'phi=54-74, psi=30-50'
_item_description.description ; The descriptor that categorizes type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsions angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conf_type.id' struct_conf_type yes '_struct_conf.conf_type_id' struct_conf yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.conf_type_id' '_struct_conf_type.id' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail HELX-RHAL 'right-handed alpha helix (protein)' HELX-RHGA 'right-handed gamma helix (protein)' HELX-RHOM 'right-handed omega helix (protein)' HELX-RHPI 'right-handed pi helix (protein)' HELX-RH3T 'right-handed 3-10 helix (protein)' HELX-LHAL 'left-handed alpha helix (protein)' HELX-LHGA 'left-handed gamma helix (protein)' HELX-LHOM 'left-handed omega helix (protein)' HELX-LHPI 'left-handed pi helix (protein)' HELX-LH3T 'left-handed 3-10 helix (protein)' HELX-PPRO 'polyproline (protein)' HELX-OTHR 'helix other (protein)' HELX-RHA 'right-handed A helix (nucleic acid)' HELX-RHB 'right-handed B helix (nucleic acid)' HELX-RHZ 'right-handed Z helix (nucleic acid)' HELX-RHO 'right-handed other helix (nucleic acid)' HELX-LHA 'left-handed A helix (nucleic acid)' HELX-LHB 'left-handed B helix (nucleic acid)' HELX-LHZ 'left-handed Z helix (nucleic acid)' HELX-LHO 'left-handed other helix (nucleic acid)' TURN-TY1 'type I turn (protein)' TURN-TY1P 'type 1 prime turn (protein)' TURN-TY2 'type II turn (protein)' TURN-TY2P 'type II prime turn (protein)' TURN-TY3 'type III turn (protein)' TURN-TY3P 'type III prime turn (protein)' TURN-OTHR 'turn other (protein)' STRN 'beta strand (protein)'
_item_description.description ; The descriptor that categorizes type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsions angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conf_type.id' struct_conf_type yes '_struct_conf.conf_type_id' struct_conf yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.conf_type_id' '_struct_conf_type.id' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail HELX-RHAL 'right-handed alpha helix (protein)' HELX-RHGA 'right-handed gamma helix (protein)' HELX-RHOM 'right-handed omega helix (protein)' HELX-RHPI 'right-handed pi helix (protein)' HELX-RH3T 'right-handed 3-10 helix (protein)' HELX-LHAL 'left-handed alpha helix (protein)' HELX-LHGA 'left-handed gamma helix (protein)' HELX-LHOM 'left-handed omega helix (protein)' HELX-LHPI 'left-handed pi helix (protein)' HELX-LH3T 'left-handed 3-10 helix (protein)' HELX-PPRO 'polyproline (protein)' HELX-OTHR 'helix other (protein)' HELX-RHA 'right-handed A helix (nucleic acid)' HELX-RHB 'right-handed B helix (nucleic acid)' HELX-RHZ 'right-handed Z helix (nucleic acid)' HELX-RHO 'right-handed other helix (nucleic acid)' HELX-LHA 'left-handed A helix (nucleic acid)' HELX-LHB 'left-handed B helix (nucleic acid)' HELX-LHZ 'left-handed Z helix (nucleic acid)' HELX-LHO 'left-handed other helix (nucleic acid)' TURN-TY1 'type I turn (protein)' TURN-TY1P 'type 1 prime turn (protein)' TURN-TY2 'type II turn (protein)' TURN-TY2P 'type II prime turn (protein)' TURN-TY3 'type III turn (protein)' TURN-TY3P 'type III prime turn (protein)' TURN-OTHR 'turn other (protein)' STRN 'beta strand (protein)'
save_struct_conf_type.reference.
_item_description.description ; A literature reference that defines the criteria used to assign this conformation type and subtype. ; _item.name '_struct_conf_type.reference' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'Kabsch and Sander, ref?'
_category.description ; Data items in the STRUCT_CONN category record details about the interactions between portions of structure. These can be hydrogen bonds, salt bridges, disulfide bridges, and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these contacts. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_conn.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.ptnr1_label_res_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_role _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_res_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_role _struct_conn.ptnr2_symmetry _struct_conn.details C1 saltbr ARG A 87 NZ1 positive 1_555 GLU A 92 OE1 negative 1_555 . C2 hydrog ARG B 287 N donor 1_555 GLY B 292 O acceptor 1_555 . # - - - - data truncated for brevity - - - - ;
_item_description.description ; A description of special aspects of the connect item. ; _item.name '_struct_conn.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'disulfide bridge C-S-S-C is highly distorted' 'another example'
_item_description.description ; The value of _struct_conn.id must uniquely identify a record in the STRUCT_CONN list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_conn.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
save_struct_conn.ptnr1_label_alt_id.
_item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_conn.ptnr1_label_asym_id.
_item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_conn.ptnr1_label_atom_id.
_item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ;
save_struct_conn.ptnr1_label_res_id.
_item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_conn.ptnr1_label_seq_id.
_item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
_item_description.description ; The chemical or structural role of the the first partner in the structure connection. ; _item.name '_struct_conn.ptnr1_role' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'donor' 'acceptor' 'negative' 'positive' 'metal' 'metal coordination'
save_struct_conn.ptnr1_symmetry.
_item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr1_label* to generate the first partner in the structure connection. ; _item.name '_struct_conn.ptnr1_symmetry' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
save_struct_conn.ptnr2_label_alt_id.
_item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_conn.ptnr2_label_asym_id.
_item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_conn.ptnr2_label_atom_id.
_item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ;
save_struct_conn.ptnr2_label_res_id.
_item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_conn.ptnr2_label_seq_id.
_item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
_item_description.description ; The chemical or structural role of the the second partner in the structure connnection. ; _item.name '_struct_conn.ptnr2_role' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'donor' 'acceptor' 'negative' 'positive' 'metal' 'metal coordination'
save_struct_conn.ptnr2_symmetry.
_item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr2_label* to generate the second partner in the structure connection. ; _item.name '_struct_conn.ptnr2_symmetry' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
_category.description ; Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of structure. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_conn_type.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference saltbr 'negative to positive distance > 2.5 \%A, < 3.2 \%A' . hydrog 'N to O distance > 2.5 \%A, < 3.5 \%A, N O C angle < 120 degrees' . ;
save_struct_conn_type.criteria.
_item_description.description ; The criteria used to define the interaction. ; _item.name '_struct_conn_type.criteria' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'O to N distance > 2.5 \%A, < 3.2 \%A' 'authors judgement'
_item_description.description ; The chemical or structural type of the interaction. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conn_type.id' struct_conn_type yes '_struct_conn.conn_type_id' struct_conn yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conn.conn_type_id' '_struct_conn_type.id' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail covale 'covalent bond' disulf 'disulfide bridge' hydrog 'hydrogen bond' metalc 'metal coordination' mismat 'mismatched base pairs' saltbr 'ionic interaction'
_item_description.description ; The chemical or structural type of the interaction. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conn_type.id' struct_conn_type yes '_struct_conn.conn_type_id' struct_conn yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conn.conn_type_id' '_struct_conn_type.id' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail covale 'covalent bond' disulf 'disulfide bridge' hydrog 'hydrogen bond' metalc 'metal coordination' mismat 'mismatched base pairs' saltbr 'ionic interaction'
save_struct_conn_type.reference.
_item_description.description ; A reference that specifies the criteria used to define the interaction. ; _item.name '_struct_conn_type.reference' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description ; Data items in the STRUCT_MON_CIS category record identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in _struct_mon_details.prot_cis. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_mon_prot_cis.label_alt_id' '_struct_mon_prot_cis.label_asym_id' '_struct_mon_prot_cis.label_res_id' '_struct_mon_prot_cis.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
_category.description ; Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summaries in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in various maps calculations, the radii used for including points in a calculation, etc. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_mon_details.block_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
save_struct_mon_details.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; This data item describes the specifics of the calculations that generated the values given in given in _struct_mon_prot.RSCC_all, _struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for inclusion of map grid points in the calculation. ; _item.name '_struct_mon_details.RSCC' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item.examples.case ; The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Maps grid points within 1.5 A of the designated atoms were included in the calculation. ; ; The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure factor amplitudes and phases, respectively, calculated from the current model. Maps grid points within a van der Waals radius of the designated atoms were included in the calculation. ;
_item_description.description ; This data item describes the specifics of the calculations that generated the values given in given in _struct_mon_prot.RSR_all, _struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for inclusion of map grid points in the calculation. ; _item.name '_struct_mon_details.RSR' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item.examples.case ; The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Maps grid points within 1.5 A of the designated atoms were included in the calculation. ; ; The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure factor amplitudes and phases, respectively, calculated from the current model. Maps grid points within a van der Waals radius of the designated atoms were included in the calculation. ;
_category.description . _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_mon_nucl.label_alt_id' '_struct_mon_nucl.label_asym_id' '_struct_mon_nucl.label_res_id' '_struct_mon_nucl.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case
_item_description.description ; The value in degrees of the backbone torsion angle alpha o3'_p_o5'_c5'. ; _item.name '_struct_mon_nucl.alpha' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the backbone torsion angle beta p_o5'_c5'_c4'. ; _item.name '_struct_mon_nucl.beta' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the sugar-base torsion angle chi o4'_c1'_n1_c2. ; _item.name '_struct_mon_nucl.chi1' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the sugar-base torsion angle chi o4'_c1'_n9_c4. ; _item.name '_struct_mon_nucl.chi2' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the backbone torsion angle delta c5'_c4'_c3'_o3'. ; _item.name '_struct_mon_nucl.delta' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; A description of special aspects of the residue, its conformation, behavior in refinement, or any other aspect that requires annotation. ; _item.name '_struct_mon_nucl.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item.examples.case ; Part of the phosphodiester backbone not in density. ;
_item_description.description ; The value in degrees of the backbone torsion angle epsilon c4'_c3'_o3'_p. ; _item.name '_struct_mon_nucl.epsilon' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the backbone torsion angle gamma o5'_c5'_c4'_c3'. ; _item.name '_struct_mon_nucl.gamma' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
save_struct_mon_nucl.label_alt_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_mon_nucl.label_asym_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_mon_nucl.label_res_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_mon_nucl.label_seq_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
save_struct_mon_nucl.mean_B_all.
_item_description.description ; The mean value of the isotropic temperature factor for all atoms in the monomer. ; _item.name '_struct_mon_nucl.mean_B_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.mean_B_base.
_item_description.description ; The mean value of the isotropic temperature factor for atoms in the base moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_base' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.mean_B_phos.
_item_description.description ; The mean value of the isotropic temperature factor for atoms in the phosphate moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_phos' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.mean_B_sugar.
_item_description.description ; The mean value of the isotropic temperature factor for atoms in the sugar moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_sugar' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description ; The value in degrees of the sugar torsion angle nu0 c4'_o4'_c1'_c2'. ; _item.name '_struct_mon_nucl.nu0' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the sugar torsion angle nu1 o4'_c1'_c2'_c3'. ; _item.name '_struct_mon_nucl.nu1' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the sugar torsion angle nu2 c1'_c2'_c3'_c4'. ; _item.name '_struct_mon_nucl.nu2' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the sugar torsion angle nu3 c2'_c3'_c4'_o4'. ; _item.name '_struct_mon_nucl.nu3' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the sugar torsion angle nu4 c3'_c4'_o4'_c1'. ; _item.name '_struct_mon_nucl.nu4' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
save_struct_mon_nucl.RSCC_all.
_item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard, Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the nucleic acid monomer. SUM [p(o) -] * SUM [p(c) -
] RSCC = ------------------------------------------------------ SQRT {SUM[(p(o) -
)^2] * SUM[(p(c) -
)^2]} where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), < > indicates an average and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSCC_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.RSCC_base.
_item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard, Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the base moiety of the nucleic acid monomer. SUM [p(o) -] * SUM [p(c) -
] RSCC = ------------------------------------------------------ SQRT {SUM[(p(o) -
)^2] * SUM[(p(c) -
)^2]} where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), < > indicates an average and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSCC_base' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.RSCC_phos.
_item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard, Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. SUM [p(o) -] * SUM [p(c) -
] RSCC = ------------------------------------------------------ SQRT {SUM[(p(o) -
)^2] * SUM[(p(c) -
)^2]} where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), < > indicates an average and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSCC_phosphodiester' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.RSCC_sugar.
_item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard, Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the sugar moiety of the nucleic acid monomer. SUM [p(o) -] * SUM [p(c) -
] RSCC = ------------------------------------------------------ SQRT {SUM[(p(o) -
)^2] * SUM[(p(c) -
)^2]} where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), < > indicates an average and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSCC_sugar' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description ; The real-space residual RSR, as described by C.I. Branden and T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms in the nucleic acid monomer. RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)] where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSR_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.RSR_base.
_item_description.description ; The real-space residual RSR, as described by C.I. Branden and T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms in the base moiety of the nucleic acid monomer. RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)] where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSR_base' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.RSR_phos.
_item_description.description ; The real-space residual RSR, as described by C.I. Branden and T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)] where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSR_phosphodiester' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_nucl.RSR_sugar.
_item_description.description ; The real-space residual RSR, as described by C.I. Branden and T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms in the sugar moiety of the nucleic acid monomer. RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)] where p(o) is the density in a map calculated with amplitude F(o) and phase alpha(c), p(c) is the density in a map calculated with amplitude F(c) and phase alpha(c), and the sums are taken over all map grid points near the relevant atoms. ; _item.name '_struct_mon_nucl.RSR_sugar' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description ; The value in degrees of the backbone torsion angle zeta c3'_o3'_p_o5'. ; _item.name '_struct_mon_nucl.zeta' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_category.description ; Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analysed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, the details of the method of calculation are described in data items in the STRUCT_MON_DETAILS category. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_mon_prot.label_alt_id' '_struct_mon_prot.label_asym_id' '_struct_mon_prot.label_res_id' '_struct_mon_prot.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
_item_description.description ; The value in degrees of the side chain torsion angle chi1, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi1' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the side chain torsion angle chi2, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi2' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the side chain torsion angle chi3, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi3' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the side chain torsion angle chi4, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi4' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the side chain torsion angle chi5, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi5' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; A description of special aspects of the residue, its conformation, behavior in refinement, or any other aspect that requires annotation. ; _item.name '_struct_mon_prot.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float loop_ _item.examples.case 'very poor density' ; The side chain of this density may occupy alternative conformations, but alternative conformations were not fit in this model ; ; This residue has a close contact with the bound inhibitor, which may account for the non-standard conformation of the side chain. ;
save_struct_mon_prot.label_alt_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_mon_prot.label_asym_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_mon_prot.label_res_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_mon_prot.label_seq_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
save_struct_mon_prot.mean_B_all.
_item_description.description ; The mean value of the isotropic temperature factor for all atoms in the monomer. ; _item.name '_struct_mon_prot.mean_B_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_prot.mean_B_main.
_item_description.description ; The mean value of the isotropic temperature factor for atoms in the main chain of the monomer. ; _item.name '_struct_mon_prot.mean_B_main' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_prot.mean_B_side.
_item_description.description ; The mean value of the isotropic temperature factor for atoms in the side chain of the monomer. ; _item.name '_struct_mon_prot.mean_B_side' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description ; The value in degrees of the main chain torsion angle omega. ; _item.name '_struct_mon_prot.omega' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the main chain torsion angle phi. ; _item.name '_struct_mon_prot.phi' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the main chain torsion angle psi. ; _item.name '_struct_mon_prot.psi' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
save_struct_mon_prot.RSCC_all.
_item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard, Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the monomer. SUM [p(o) -] * SUM [p(c) -
] RSCC = ------------------------------------------------------ SQRT {SUM[(p(o) -
)^2] * SUM[(p(c) -
)^2]} where p(o) is the density in an "experimental" map and p(c) is the density in a "calculated" map. The details of how these maps were calculated should be described in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon.details_RSCC. ; _item.name '_struct_mon_prot.RSCC_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_prot.RSCC_main.
_item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard, Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the main chain of the monomer. SUM [p(o) -] * SUM [p(c) -
] RSCC = ------------------------------------------------------ SQRT {SUM[(p(o) -
)^2] * SUM[(p(c) -
)^2]} where p(o) is the density in an "experimental" map and p(c) is the density in a "calculated" map. The details of how these maps were calculated should be described in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon.details_RSCC. ; _item.name '_struct_mon_prot.RSCC_main' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_prot.RSCC_side.
_item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard, Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the side chain of the monomer. SUM [p(o) -] * SUM [p(c) -
] RSCC = ------------------------------------------------------ SQRT {SUM[(p(o) -
)^2] * SUM[(p(c) -
)^2]} where p(o) is the density in an "experimental" map and p(c) is the density in a "calculated" map. The details of how these maps were calculated should be described in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon.details_RSCC. ; _item.name '_struct_mon_prot.RSCC_side' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description ; The real-space residual RSR, as described by C.I. Branden and T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms in the monomer. SUM [p(o) - p(c)] RSR = ----------------- SUM [p(o) + p(c)] where p(o) is the density in an "experimental" map and p(c) is the density in a "calculated" map. The details of how these maps were calculated should be described in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon.details_RSR. ; _item.name '_struct_mon_prot.RSR_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_prot.RSR_main.
_item_description.description ; The real-space residual RSR, as described by C.I. Branden and T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms in the main chain of the monomer. SUM [p(o) - p(c)] RSR = ----------------- SUM [p(o) + p(c)] where p(o) is the density in an "experimental" map and p(c) is the density in a "calculated" map. The details of how these maps were calculated should be described in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon.details_RSR. ; _item.name '_struct_mon_prot.RSR_main' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_prot.RSR_side.
_item_description.description ; The real-space residual RSR, as described by C.I. Branden and T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms in the main chain of the monomer. SUM [p(o) - p(c)] RSR = ----------------- SUM [p(o) + p(c)] where p(o) is the density in an "experimental" map and p(c) is the density in a "calculated" map. The details of how these maps were calculated should be described in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon.details_RSR. ; _item.name '_struct_mon_prot.RSR_side' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
save_struct_mon_prot_cis.label_alt_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_mon_prot_cis.label_asym_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_mon_prot_cis.label_res_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_mon_prot_cis.label_seq_id.
_item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
_category.description ; Data items in the STRUCT_NCS_DOM record information about the domains in an ensemble of domains related by non-crystallographic symmetry. A domain need not correponds to a poly-peptide chains - it can be composed of segments of a single chain, or segments of more than one chain. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_ncs_dom.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
_item_description.description ; A description of special aspects of the structural elements that comprise a domain in an emsemble of domains related by non- crystallographic symmetry. ; _item.name '_struct_ncs_dom.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; The loop between residues 18 and 23 in this domain interacts with a symmetry related molecule, and thus deviates significantly from the non-crystallographic 3-fold. ;
_item_description.description ; The value of _struct_ncs_dom.id must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_dom.id' struct_ncs_dom yes '_struct_ncs_ens_gen.dom_id_1' struct_ncs_ens_gen yes '_struct_ncs_ens_gen.dom_id_2' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_dom.id' '_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_dom.id' _item_type.code char
_item_description.description ; The value of _struct_ncs_dom.id must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_dom.id' struct_ncs_dom yes '_struct_ncs_ens_gen.dom_id_1' struct_ncs_ens_gen yes '_struct_ncs_ens_gen.dom_id_2' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_dom.id' '_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_dom.id' _item_type.code char
_item_description.description ; The value of _struct_ncs_dom.id must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_dom.id' struct_ncs_dom yes '_struct_ncs_ens_gen.dom_id_1' struct_ncs_ens_gen yes '_struct_ncs_ens_gen.dom_id_2' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_dom.id' '_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_dom.id' _item_type.code char
_category.description ; Data items in the STRUCT_NCS_DOM_GEN category identify the structural elements thats comprise a domain in an ensemble of domains related by non-crystallographic symmetry. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_ncs_dom_gen.dom_id' '_struct_ncs_dom_gen.beg_label_alt_id' '_struct_ncs_dom_gen.beg_label_asym_id' '_struct_ncs_dom_gen.beg_label_res_id' '_struct_ncs_dom_gen.beg_label_seq_id' '_struct_ncs_dom_gen.end_label_alt_id' '_struct_ncs_dom_gen.end_label_asym_id' '_struct_ncs_dom_gen.end_label_res_id' '_struct_ncs_dom_gen.end_label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
save_struct_ncs_dom_gen.beg_label_alt_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_ncs_dom_gen.beg_label_asym_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_ncs_dom_gen.beg_label_res_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_ncs_dom_gen.beg_label_seq_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
save_struct_ncs_dom_gen.dom_id.
_item_description.description ; This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ;
save_struct_ncs_dom_gen.end_label_alt_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_ncs_dom_gen.end_label_asym_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_ncs_dom_gen.end_label_res_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_ncs_dom_gen.end_label_seq_id.
_item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
_category.description ; Data items in the STRUCT_NCS_ENS category record information about ensembles of structural element related by non- crystallographic symmetry (ncs), such as the point group of the ensemble when taken as a whole, and any special aspects of it that require description. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_ncs_ens.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
_item_description.description ; A description of special aspects of the connect item. ; _item.name '_struct_ncs_ens.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; The ensemble has a slight translation between domains 1 and 4, but overall it can accurately be described as point group 222 ;
_item_description.description ; The value of _struct_ncs_ens.id must uniquely identify a record in the STRUCT_NCS_ENS list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_ens.id' struct_ncs_ensemble yes '_struct_ncs_ens_gen.ens_id' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.ens_id' '_struct_ncs_ens.id' _item_type.code char
_item_description.description ; The value of _struct_ncs_ens.id must uniquely identify a record in the STRUCT_NCS_ENS list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_ens.id' struct_ncs_ensemble yes '_struct_ncs_ens_gen.ens_id' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.ens_id' '_struct_ncs_ens.id' _item_type.code char
save_struct_ncs_ens.point_group.
_item_description.description ; The point group of the ensemble of structural elements related by non crystallographic symmetry. The relationships need not be precise; this data items is intended to give a rough description of the non-crystallographic symmetry relationships. ; _item.name '_struct_ncs_ens.point_group' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '3' '422' 'non-proper'
_category.description ; Data items in the STRUCT_NCS_ENS_GEN category describe the operations that result in the superposition of one domain in an ensembled of domains related by non-crystallographic symmetry upon a second domain in the ensemble. %%% %%% Note - I have only added data items for the polar angles that describe %%% the operation - we are probably going to need some vector component to %%% this as well, and this will take some thought and consultation %%% ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_ncs_ens_oper.ens_id' '_struct_ncs_ens_oper.dom_id_1' '_struct_ncs_ens_oper.dom_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; Need example 1 ;
save_struct_ncs_ens_oper.details.
_item_description.description ; A description of special aspects of the transformation operation. ; _item.name '_struct_ncs_ens_oper.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; The operation is given a precise threefold rotation, despite the fact the the best rms fit between domain 1 and domain 2 yields a rotation of 119.7 angles and a translation of 0.13 angstroms. ;
save_struct_ncs_ens_oper.dom_id_1.
_item_description.description ; The identifier for the domain that will remain unchanged by the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ;
save_struct_ncs_ens_oper.dom_id_2.
_item_description.description ; The identifier for the domain that will be transformed by application of the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ;
save_struct_ncs_ens_oper.ens_id.
_item_description.description ; This data item is a pointer to _struct_ncs_ens.id in the STRUCT_NCS_ENS category. ;
save_struct_ncs_ens_oper.kappa.
_item_description.description ; The rotation in degrees about the symmetry axis. %%% %%% Need more precise definition here. %%% ; _item.name '_struct_ncs_ens_oper.kappa' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The angle that the symmetry axis makes with the xz plane of the refence coordinate system. %%% %%% Need more precise definition here. %%% ; _item.name '_struct_ncs_ens_oper.phi' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The angle that the symmetry axis makes with the z axis of the refence coordinate system. %%% %%% Need more precise definition here. %%% ; _item.name '_struct_ncs_ens_oper.psi' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_category.description ; Data items in the STRUCT_SITE category record details about portions of structure that contribute to certain structurally relevant sites (i.e., active sites, substrate-binding subsites, metal-coordination sites). ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_site.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_site.id _struct_site.details 'P2 site C' ; residues with a contact < 3.7 \%A to an atom in the P2 moiety of the inhibitor in the conformation with _struct_asym.id = C ; 'P2 site D' ; residues with a contact < 3.7 \%A to an atom in the P1 moiety of the inhibitor in the conformation with _struct_asym.id = D) ; ;
_item_description.description ; A description of special aspects of the structural site. ; _item.name '_struct_site.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; ??? ;
_item_description.description ; The value of _struct_site.id must uniquely identify a record in the STRUCT_SITE list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_site.id' struct_site yes '_struct_site_gen.site_id' struct_site_gen yes '_struct_site_keywords.site_id' struct_site_keywords yes '_struct_site_view.site_id' struct_site_view yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_site_gen.site_id' '_struct_site.id' '_struct_site_keywords.site_id' '_struct_site.id' '_struct_site_view.site_id' '_struct_site.id' _item_type.code char
_category.description ; Data items in the STRUCT_SITE_GEN category record details about the generation of portions of structure that contribute to structurally relevant sites. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_site_gen.id' '_struct_site_gen.site_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.label_res_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.symmetry _struct_site_gen.details 1 1 VAL A 32 1_555 . 2 1 ILE A 47 1_555 . 3 1 VAL A 82 1_555 . 4 1 ILE A 84 1_555 . 5 2 VAL B 232 1_555 . 6 2 ILE B 247 1_555 . 7 2 VAL B 282 1_555 . 8 2 ILE B 284 1_555 . ;
_item_description.description ; A description of special aspects of the symmetry generation of this portion of the structural site. ; _item.name '_struct_site_gen.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. ;
_item_description.description ; The value of _struct_site_gen.id must uniquely identify a record in the STRUCT_SITE_GEN list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_site_gen.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
save_struct_site_gen.label_alt_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ;
save_struct_site_gen.label_asym_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ;
save_struct_site_gen.label_atom_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _entity_mon_atom.atom_id in the ENTITY_MON_ATOM category. ;
save_struct_site_gen.label_res_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _entity_mon.id in the ENTITY_MON category. ;
save_struct_site_gen.label_seq_id.
_item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ;
_item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ;
save_struct_site_gen.symmetry.
_item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_site_gen.label* to generate a portion of the structure site. ; _item.name '_struct_site_gen.symmetry' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y'
_category.description ; Data items in the STRUCT_SITE_KEYWORDS category... ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_site_keywords.site_id' '_struct_site_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_site_keywords.site_id _struct_site_keywords.text 'P2 site C' 'binding site' 'P2 site C' 'binding pocket' 'P2 site C' 'P2 site' 'P2 site C' 'P2 pocket' 'P2 site D' 'binding site' 'P2 site D' 'binding pocket' 'P2 site D' 'P2 site' 'P2 site D' 'P2 pocket' ;
save_struct_site_keywords.site_id.
_item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ;
save_struct_site_keywords.text.
_item_description.description ; Keywords describing this structural site. ; _item.name '_struct_site_keywords.text' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'active site' 'binding pocket' 'Ca coordination'
_category.description ; Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate a useful didactic view of the structural site. ; _category.id _category.id _category.mandatory_code no _category_key.name '_struct_site_view.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on ; ; Need Example 1 ;
save_struct_site_view.details.
_item_description.description ; A description of special aspects of this view of the structural site. This data item can be used as a figure legend, if desired. ; _item.name '_struct_site_view.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; The active site has been oriented with the specificity pocket on the right and the active site machinery on the left. ;
_item_description.description ; The value of _struct_site_view.id must uniquely identify a record in the STRUCT_SITE_VIEW list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_site_view.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Figure 1' 'unliganded enzyme' 'view down enzyme active site'
save_struct_site_view.rot_matrix.
_item_description.description ; The matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_VIEW_GEN category to a view useful for describing the structural site. The conventions used in the rotation are described in _struct_site_view.details. |11 12 13| x x' |21 22 23| ( y ) Cartesian = ( y' ) reoriented Cartesian |31 32 33| z z' ; _item.name '_struct_site_view.rot_matrix' _item.category_id _item.category_id _item.mandatory_code no _item_structure.code 'matrix3x3' _item_structure.organization 'rowwise' _item_type.code float
save_struct_site_view.site_id.
_item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ;
_category.description ; Data items in the SYMMETRY category record details about the space-group symmetry. ; _category.id _category.id _category.mandatory_code no _category_key.name '_symmetry.block_id' loop_ _category_group.id 'inclusive_group' 'symmetry_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 18 _symmetry.space_group_name_H-M 'P 21 21 2' ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _symmetry.cell_setting orthorhombic _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.space_group_name_Hall P_2ac_2ab ;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The cell settings for this space-group symmetry. ; _item.name '_symmetry.cell_setting' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_symmetry_cell_setting' _item_type.code char loop_ _item_enumeration.value triclinic monoclinic orthorhombic tetragonal rhombohedral trigonal hexagonal cubic
save_symmetry.Int_Tables_number.
_item_description.description ; Space-group number from International Tables for Crystallography, Vol. A (1987). ; _item.name '_symmetry.Int_Tables_number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_symmetry_Int_Tables_number' _item_type.code int
save_symmetry.space_group_name_H-M.
_item_description.description ; Hermann-Mauguin space-group symbol. Note that the H-M symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used always supply the FULL symbol from International Tables for Crystallography, Vol. A (1987) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol specify the _symmetry.equiv_pos_as_xyz or _symmetry.space_group_name_Hall data items as well. Leave spaces between symbols referring to different axes. ; _item.name '_symmetry.space_group_name_H-M' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_symmetry_space_group_name_H-M' _item_type.code char loop_ _item_examples.case 'P 1 21/m 1' 'P 2/n 2/n 2/n (origin at -1)' 'R -3 2/m'
save_symmetry.space_group_name_Hall.
_item_description.description ; Hall space-group symbol [Hall, S. R. (1981). Acta Cryst. A37, 517-525]. This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. ; _item.name '_symmetry.space_group_name_Hall' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_symmetry_space_group_name_Hall' _item_type.code char loop_ _item_examples.case '-P 2ac 2n' '-R 3 2"' 'P 61 2 2 (0 0 -1)'
_category.description ; Data items in the SYMMETRY_EQUIV category list the symmetry equivalent positions for the space group. ; _category.id _category.id _category.mandatory_code no _category_key.name '_symmetry_equiv.id' loop_ _category_group.id 'inclusive_group' 'symmetry_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 '+x,+y,+z' 2 '-x,-y,z' 3 '1/2+x,1/2-y,-z' 4 '1/2-x,1/2+y,-z' ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _symmetry_equiv.pos_as_xyz +x,+y,+z 1/2-x,-y,1/2+z 1/2+x,1/2-y,-z -x,1/2+y,1/2-z ;
_item_description.description ; The value of _symmetry_equiv.id must uniquely identify a record in the SYMMETRY_EQUIV category. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_symmetry_equiv.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char
save_symmetry_equiv.pos_as_xyz.
_item_description.description ; Symmetry equivalent position in the 'xyz' representation. Except for the space group P1, this data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography, Vol. A. (1987). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present. ; _item.name '_symmetry_equiv.pos_as_xyz' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_symmetry_equiv_pos_as_xyz' _item_type.code char _item_examples.case -y+x,-y,1/3+z