Acta Cryst. (1999). D55, 363-368

International Union of Crystallography

Acta Crystallographica Section D

Notes for Authors 1999

1. Scientific scope of Section D

Section D of Acta Crystallographica welcomes the submission of papers covering any aspect of biological crystallography, particularly structures of biological macromolecules. In addition to new structural determinations, preliminary data on unit-cell dimensions and space groups will be considered for publication, provided suitable diffraction photographs (or their equivalent), together with an estimate of resolution, are included. Also, articles on crystal growth of biological macromolecules are welcomed, and refinements of known structures may be published if the information content warrants it. For all structural papers, sufficient evidence should be provided to convince the referees that the interpretations of the diffraction data and electron-density maps are correct, within the resolution of the analysis.

2. Categories of contributions

3. Submission and handling of manuscripts

3.1. Submission

Manuscripts should be prepared on one side of the paper in double-spaced format. All contributions should be submitted in triplicate and authors are reminded to keep an exact copy of the submission for later editorial adjustments and for checking proofs. A machine-readable version of the final accepted manuscript will be requested by the Editorial Office, provided it can be prepared using one of the four word-processing formats listed in section 3.4. This request is designed to reduce publication times.

Every issue of the journal contains the names and addresses of the Section Editor, the Co-editors of Acta Crystallographica Section D and of the Managing Editor. This information is also available at http://www.iucr.org/actad. Contributions should be submitted as follows.

Research Papers: to any of the Co-editors having regard to their areas of expertise.

Short Communications, Fast Communications and Crystallization Papers: to the Section Editor or any of the Co-editors having regard to their areas of expertise.

Lead Articles and Topical Reviews: these will be handled by the Section Editor as described in section 2 of these Notes.

3.2. Languages of publication

Acta Crystallographica Section D will publish papers in English, French, German and Russian. All contributions must be accompanied by an English language Abstract and synopsis.

3.3. Handling of manuscripts

All contributions will be seen by referees (normally two) before they can be accepted for publication. The editor to whom the manuscript is sent is responsible for choosing referees and for accepting or rejecting the paper. This responsibility includes decisions on the final form of the paper and interpretation of these Notes when necessary.

If changes to a manuscript requested by the editorial staff or the Co-editor are not received within three months of transmittal to the author, the submission will automatically be withdrawn. Any subsequent communication of the material will be treated as a new submission in the editorial process.

For accepted papers, it is the responsibility of the Managing Editor to prepare the paper for printing. This may involve correspondence with the authors and/or the responsible editor in order to resolve ambiguities or to obtain satisfactory figures or tables. The date of acceptance that will appear on the published paper is the date on which the Managing Editor receives the last item required. Proofs will be sent to the author who signed the letter of submission unless the Managing Editor is informed of some other suitable arrangement.

On rare occasions an editor may consider that a paper is better suited to a section of Acta Crystallographica other than that specified by the author(s), to the Journal of Applied Crystallographyor to the Journal of Synchrotron Radiation. Any change to the section or journal of publication will only be made after full discussion with the communicating author.

3.4. File formats

A machine-readable version of the paper should be prepared in TeX, LaTeX or Word. Authors are encouraged to use the templates available from the Editorial Office by e-mail (med@iucr.org) or by ftp (from the `templates' directory). It would be appreciated if all Word submissions were accompanied by an RTF (rich text format) file. After acceptance of the paper for publication, authors should send the version of the paper accepted by the Co-editor to the Editorial Office by e-mail or ftp (see section 13), or on diskette.

3.5. Author's warranty

The submission of a paper is taken as an implicit guarantee that the work is original, that it is the author(s) own work, that all authors concur with and are aware of the submission, that all workers involved in the study are listed as authors or given proper credit in the acknowledgements, that the manuscript has not already been published (in any language or medium), and that it is not being considered and will not be offered elsewhere while under consideration for an IUCr journal. For these reasons, all authors will be required to sign off the final version of the paper.

3.6. Copyright

Except as required otherwise by national laws, an author must sign and submit a copy of the Transfer of Copyright Agreement form for each manuscript before it can be accepted.

3.7. Author grievance procedure

An author who believes that a paper has been unjustifiably treated by the Co-editor may appeal initially to the Section Editor and then to the Editor-in-Chief if still aggrieved by the decision.

3.8. Contact e-mail address

The contact author should, where possible, provide an e-mail address. This will be used for editorial communications and will normally appear in the published paper.

4. Layout and typography

Contributions should be prepared on one side of the paper in double-spaced format with wide margins, and should conform to the general editorial style of IUCr journals.

4.1. Type style

The editorial staff in Chester will indicate to the printer the style of type to be used. It is better that authors should not indicate type style at all rather than do so in a way different from that used by the printers. However, it is helpful if authors indicate vectors and tensors by a wavy underline.

4.2. Mathematics and letter symbols

The use of the stop (period) to denote multiplication should be avoided except in scalar products. Generally no sign is required but, when one is, a multiplication sign (×) should be used.

Greek letters should not be spelled out except in marginal notes of clarification.

Care should be taken not to cause confusion by using the same letter symbol in two different meanings.

Gothic, script or other unusual lettering should be identified in marginal notes. The printer may be instructed to use another type face if that indicated by the author is not readily available.

Equations, including those in published Appendices, should be numbered in a single series.

5. Abstract and synopsis

All contributions must be accompanied by an English language Abstract and a one or two sentence synopsis of the main findings of the paper for inclusion in the Table of Contents for the relevant issue. The Abstract should state as specifically and as quantitatively as possible the principal results obtained.

The Abstract should be suitable for reproduction by abstracting services without change in wording. It should not repeat information given in the title. Ordinarily 200 words suffice for Research Papers, Lead Articles and Topical Reviews and 100 words for Short Communications, Crystallization Papers and Fast Communications. It should make no reference to tables, diagrams, atom numbers or formulae contained in the paper. It should not contain footnotes. Numerical information given in the Abstract should not be repeated in the text. It should not include the use of `we' or `I'.

Literature references in an Abstract are discouraged. If a reference is unavoidable, it should be sufficiently full within the Abstract for unambiguous identification, e.g. [Terwilliger (1994). Acta Cryst. D50, 17-23].

6. Diagrams and photographs (`figures')

6.1. Design

The choice of tables and figures should be optimized to produce the shortest printed paper consistent with clarity. Duplicate presentation of the same information in both tables and figures is to be avoided, as is redundancy with the text.

Supplementary diagrams may be deposited (see section 12.1).

Authors of protein structure papers are requested to submit a picture of the C alpha chain trace. This will be helpful for referees and may be deposited. In addition, a diagram of the fit of a side chain is helpful to the reader in terms of assessing the resolution and map quality.

Fibre data should contain appropriate information such as a photograph of the data. As primary diffraction data cannot be satisfactorily extracted from such figures, the basic digital diffraction data should be deposited.

6.2 Quality

Diagrams must be provided in `hard-copy' form, that is, as careful drawings in black ink or as high-quality photographic copies (glazed prints, not mounted). An individual hard-copy diagram must be provided for each figure.

6.3. Colour figures

Figures in colour are accepted at no cost to the author provided that the editor agrees that they improve the understanding of the paper. They should be provided as glossy prints or slides; laser printer or photocopier output will generally be unsatisfactory for colour reproduction. Slides should be accompanied by a photocopy showing the required figure layout.

6.4. Size

Diagrams should be as small as possible consistent with legibility. If possible, each diagram should be provided on a separate sheet of about A4 International Paper Size (210 x 297 mm). They will normally be further reduced by the printer, generally so that the greatest width including lettering is less than the width of a column of the journal. Figures at greater than column width are allowed at editorial discretion.

6.5. Stereofigures

Stereofigures are welcomed in Section D. Atom labelling when included should be on both left and right views in stereo perspective.

6.6. Lettering and symbols

Fine-scale details and lettering must be large enough to be clearly legible (not less than 1.2 mm in height) after the whole diagram has been reduced to one column width.

Lettering should be kept to a minimum; distances, bond angles and torsion angles should be given as tables and descriptive matter should be placed in the legend.

6.7. Numbering and legends

Diagrams and photographs are to be numbered as figures in a single series, normally in the order in which they are referred to in the text. A list of the legends (`figure captions') is to be attached to the manuscript.

6.8. Electronic submission of figures

After acceptance of the paper for publication, authors may send figures direct to the editorial office by e-mail or ftp (see section 13).

Figures may be sent in HPGL, PostScript, encapsulated PostScript or TIFF formats. The resolution of bitmap graphics should be 1200 d.p.i. Hard-copy figures must be provided in all cases.

7. Tables

7.1. Economy in use of tables

Numerical information is generally most economically presented in tables. Text and diagrams should not be redundant with the tables.

Small tables will normally be set in type while large tables may be photographically reproduced or deposited.

Where possible, s.u. values (see section 8.1) should be provided for all numerical data e.g. unit-cell dimensions. Atomic cooordinates and structure factors of macromolecular structures should be deposited.

7.2. Design, numbering and size

Tables must be numbered in a single series of arabic numerals, normally in the order in which they are referred to in the text. They should be provided with a caption either at the top or, if the table is to be photographed, on a separate sheet.

Tables should be carefully designed to occupy a minimum of space consistent with clarity. Tables to be photographed should be prepared in single spacing, without excessive space between columns.

8. Nomenclature

8.1. Crystallographic nomenclature

Atoms of the same chemical species within an asymmetric unit should be distinguished by an appended arabic numeral. Chemical and crystallographic numbering should be in agreement wherever possible. When it is necessary to distinguish crystallographically equivalent atoms in different asymmetric units the distinction should be made by lower-case roman numeral superscripts (i.e. i, ii, iii etc.) to the original atom labels.

Authors are encouraged to follow the recommendation of the International Organization for Standardization (ISO) and use the term standard uncertainty, abbreviated s.u., in place of the traditional term estimated standard deviation [see Schwarzenbach et al. (1995). Acta Cryst. A51, 565-569]. The standard uncertainty should be expressed as a number in parentheses following the numerical result and should be on the scale of the least significant digits of the result.

Space groups should be designated by the Hermann-Mauguin symbols. Standard cell settings, as listed in Volume A of International Tables for Crystallography, should be used unless objective reasons to the contrary are stated. When a non-standard setting is used, the list of equivalent positions should be given. Hermann-Mauguin symbols should also be used for designating point groups and molecular symmetry. It is helpful if the origin used is stated explicitly where there is a choice.

The choice of axes should normally follow the recommendations of the Commission on Crystallographic Data [Kennard et al. (1967). Acta Cryst. 22, 445-449].

A symbol such as 123 or hkl without brackets is understood to be a reflection, (123) or (hkl) a plane or set of planes, [123] or [uvw] a direction, {hkl} a form and <uvw > all crystallographically equivalent directions of the type [uvw]. Other bracket notations should be explicitly defined.

For the nomenclature of crystal families, Bravais-lattice types and arithmetic classes see de Wolff et al. [Acta Cryst. (1985). A41, 278-280].

For symbols for symmetry elements and symmetry operations see de Wolff et al. [Acta Cryst. (1992). A48, 727-732].

Anisotropic displacement parameters should be reported as U values with the indices ij given as superscripts [see Trueblood et al. (1996). Acta Cryst. A52, 770-781].

For the nomenclature of structural phase transitions see Tolédano et al. [Acta Cryst. (1998), A54, 1028-1033].

8.2. Nomenclature of chemical compounds etc.

Chemical formulae and nomenclature should conform to the rules of nomenclature established by the International Union of Pure and Applied Chemistry (IUPAC), the International Union of Biochemistry and Molecular Biology (IUBMB), the International Mineralogical Association and other appropriate bodies. As far as possible the crystallographic nomenclature should correspond to the systematic name.

Any accepted trivial or non-systematic name may be retained, but the corresponding systematic (IUPAC) name should also be given.

If help on assigning systematic names is sought from advisory sources, authors are requested to indicate the source consulted.

8.3. Units

The International System of Units (SI) is used except that the angstrom (symbol Å, defined as 10^-10 m) is generally preferred to the nanometre (nm) or picometre (pm) as the appropriate unit of length. Recommended prefixes of decimal multiples should be used rather than `× 10ⁿ'.

9. References

References to published work must be indicated by giving the authors' names followed immediately by the year of publication, e.g. Neder & Schulz (1998) or (Neder & Schulz, 1998). Where there are six or more authors the reference in the text should be indicated in the form Smith et al. (1998) or (Smith et al., 1998) etc. (all authors should be included in the full list).

At the end of the paper a list giving full details of all references should be appended separately. In the reference list, entries for journals [abbreviated in the style of Chemical Abstracts (the abbreviations Acta Cryst., J. Appl. Cryst. and J. Synchrotron Rad. are exceptions)], books, multi-author books, computer programs, personal communications and undated documents should be arranged alphabetically and conform with the following style:

Andrews, M. D., Wright, H. E. & Clarke, S. A. (1999). In preparation.

Bricogne, G. (1993). Acta Cryst. D49, 37-60.

Brunger, A. T. (1992a). X-PLOR. Version 3.1. A System for X-ray Crystallography and NMR. Yale University, Connecticut, USA.

Brunger, A. T. (1992b). Nature (London), 355, 472-474.

Carter, C. W. Jr (1990). Methods: a Companion to Methods in Enzymology, Vol. 1, pp. 12-24. New York: Academic Press.

Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.

Chiang, L.-C., Cabezas, E., Calvo, J. C. & Satterthwait, A. C. (1994). In Peptides: Chemistry, Structure and Biology. Proceedings of the 13th American Peptide Symposium, edited by R. Hodges & J. A. Smith. Leiden: ESCOM.

Crowther, R. A. (1972). The Molecular Replacement Method, edited by M. G. Rossmann, pp. 173-178. New York: Gordon and Breach.

Ferguson, G., Schwan, A. L., Kalin, M. L. & Snelgrove, J. L. (1997). Acta Cryst. C53, IUC9700009.

International Union of Crystallography (1999). (IUCr) Acta Crystallographica Section D, http://www.iucr.org/actad.

Jancarik, J. & Kim, S.-H. (1991). J. Appl. Cryst. 24, 409-411.

Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.

Olsnes, S. & Pihl, A. (1982). Molecular Action of Toxins and Viruses, edited by P. Cohen & S. Van Heyningen, pp. 51-105. New York: Elsevier.

Stanlow, D. J. (1999). Acta Cryst. B55. In the press.

Strong, R. K. (1990). PhD thesis, Harvard University, USA.

Vogel, A. (1978). Textbook of Practical Organic Chemistry, 4th ed. London: Longman.

Wang, B.-C. (1985). Methods Enzymol. 115, 90-112.

Yariv, J. (1983). Personal communication.

Note that inclusive page numbers must be given.

10. Evaluation criteria

The criteria by which papers are evaluated are based on recommendations of the Commission on Biological Macromolecules.

10.1. Resolution

The effective resolution should be described clearly. Values of the internal agreement of the data, R_merge, together with the multiplicity (i.e. the average number of measurements for each reflection from which R_merge is calculated), the percentage of data with I > sigma(I) and percentage completeness of the data are required for the overall data set and the highest resolution shell together with the limits of that shell in Å. For high-quality data obtained with synchrotron radiation, values of R_merge < 20%, completeness >93% and observable data >70% should be achievable for the highest resolution shell. A complete table listing the above criteria as a function of resolution should also be submitted, but will normally be included in the supplementary material, see section 12.

10.2. Unrefined structures

Adequate experimental details should be provided to convince referees that the interpretation is correct, within the resolution of the analysis. If heavy-atom derivatives were used, sufficient data should be provided for evaluation of the quality of those derivatives. The fit of the model to the electron-density maps used to determine the structure should be shown or described by quantitative indicators, such as real-space residuals.

10.3. Refined structures

For refined structures the data required depend on the effective resolution of the analysis. The following should be included.

A final Ramachandran plot is important and this or a related conformational analysis should be provided for review purposes. The paper should include a brief statement of the percentage of amino acids in allowed, additionally allowed and disallowed regions of the plot.

The r.m.s. deviations in B values within each residue's main-chain and side-chain atoms should be included.

The crystallographic R index should be tabulated as a function of resolution. The value for all reflections should be given along with any other values based on selected data. R_free should also be included.

Adequate details should be provided regarding the steps followed in constructing the model and refining the structure. The number of solvent atoms should be given along with information regarding solvent B values, and the approach that was used to identify solvent sites. The report should include the history and salient details of the refinement methods employed, including the resolution ranges that were used at various stages of refinement; the restraints used; a description of how the thermal parameters were treated; and how the solvent sites were selected and handled during refinement. It should be clear if van der Waals distances were restrained, either explicitly or by energy-minimization methods.

Hydrogen-bonding patterns within the protein should be described. The number of hydrogen-bond donors that are not involved in hydrogen bonding should be given with particular attention to unsatisfied buried main-chain hydrogen bonds.

Deviations of bond lengths, bond angles and planes from ideal geometries should be given. Close intramolecular and intermolecular van der Waals contacts should be described. The character and stereochemistry of major crystal contacts should be discussed.

Any structural features that are considered somewhat unusual should be described. Examples include cis peptide bonds; unoccupied volume inside the protein, buried charge groups that are not involved in salt bridges or reasonable hydrogen-bonding environments; unusual locations of glycine and proline residues; and unusual distributions of polar and hydrophobic groups within the molecule.

11. Small-molecule structure determinations

Papers which report the results of crystal structure determinations of small molecules must report the associated numerical data as required in Notes for Authors for Section C of Acta Crystallographica . These data should be supplied in a machine-readable file in CIF format. All numerical data will be checked in Chester for internal consistency.

12. Supplementary publication procedure (deposition)

12.1. Purpose and scope

Parts of some papers are of interest to only a small number of readers, and the cost of printing these parts is not warranted. Arrangements have therefore been made for such material to be deposited with the IUCr, with the Protein Data Bank and the ICDD as appropriate.

Authors are encouraged to submit material for deposit in electronic format. The information to be deposited is at the discretion of the editor and may include:

Details of the experimental procedure.
Details of the stages of structure refinement.
Details of mathematical derivations given only in outline in the main text and in mathematical Appendices.
Lengthy discussion of points that are not of general interest or that do not lead to definite conclusions but that do have significant value.
Additional diagrams.

For papers reporting results of crystal structure determinations the following additional items are required:

Normal intermolecular distances.
Structure factors; weak reflections classified as unobserved should be included.
Anisotropic displacement parameters where relevant, including s.u.'s.
Least-squares planes and deviations from them.
Calculated H-atom coordinates if relevant.

All material to be deposited should be clearly so marked; it will be subject to the usual refereeing procedure.

12.2. Preparation of material for deposit

Authors should note that data in CIF format will be automatically archived. Material included in the CIF need not be supplied as hard copy. Hard-copy material for deposit should:

be of a quality such that photocopies of it are completely legible;
have dimensions for text and tables not exceeding A4 International Paper Size (210 x 297 mm) (larger dimensions may be acceptable in exceptional circumstances);
not be photographically reduced so that character heights are less than 1.2 mm;
contain the title page of the paper to which it relates (including the Abstract);
have pages clearly numbered to ensure the correct sequence;
be sent in triplicate with the paper when it is submitted.

After acceptance of the paper for publication, material for deposition may be sent direct to the editorial office by e-mail or ftp (see section 13).

12.3. Macromolecular structures

Data deposited should correspond to the level of detail described in the structural paper. For all structural studies of macromolecules, coordinates and structure factors must be deposited with the Protein Data Bank if a total molecular structure has been reported. Authors should supply the Protein Data Bank reference codes for inclusion in the published paper.

13. File transfer

After acceptance of the paper for publication, authors with computer access to the Internet may use anonymous file transfer protocol (ftp) to transfer large electronic files to the editorial office in Chester. Files larger than 70K bytes should be transferred in this way, smaller files can be sent by e-mail to med@iucr.org .

The procedure for transferring files by ftp is described below. Files need to be deposited in a directory called `incoming/d' with a filename constructed from the reference number supplied by the Co-editor. Files containing text in TeX or LaTeX should be given the extension .tex, Word files should be given the extension .doc and RTF files .rtf. Files containing diagrams in HPGL, PostScript, encapsulated PostScript or TIFF format should be given the extensions .hpg, .ps, .eps or .tif, respectively. Multiple files for the same submission should be identified by filenames constructed as ref.id.ext where id indicates the contents, e.g. xz1087.fig1.ps and xz1087.fig2.ps.

The procedure for transferring files is given below.

(i) On your workstation enter: ftp ftp.iucr.org

(ii) Wait for Name ...: prompt and enter: anonymous

(iii) Wait for Password: prompt
and enter: your e-mail address

(iv) Wait for ftp> prompt and enter: cd incoming/d

(v) Transfer a file from your account
(e.g. j29.ps) as an identifiable name
(e.g. ja0325.ps): put j29.ps ja0325.ps

(vi) Wait for ftp> prompt before sending another file

(vii) Finish off the ftp session by entering: bye

(viii) Send an e-mail to Chester (med@iucr.org) with a list of the files transferred by ftp

14. Electronic status information

Authors may obtain information about the current status of their papers via the World-Wide Web at the address http://www.iucr.org/iucr-top/docs/status.html/ (authors will need to provide the Co-editor reference number of their paper and the last name of one of the authors) or by e-mail by sending an e-mail message to status@iucr.org with the Co-editor reference number and the name of one of the authors as the subject line (e.g. JA0325 Smith). The body of the message should be empty. A status report will be returned by e-mail.

15. Reprints

Twenty-five reprints of each published article will be provided to a nominated author free of charge.