Meeting report

ACA 2012

Boston, MA, USA, July 2012
www. amercrystalassn.org
taken from ACA RefleXions, Fall 2012

[ACA2012 logo]

The 2012 Annual Meeting was held in Boston, Mass., July 28 through August 1. 785 participants presented 258 posters and 294 lectures. Thirty-nine exhibitors participated in the Exhibit Show, beginning with the Opening Reception on Saturday and running through Tuesday. Attendees traveled from 30 counties with 23% coming from outside the USA. Young scientists (students and post-docs) represented 32% of the total meeting attendance. The meeting was financially supported by 33 organizations whose contributions were used to support young scientists, speakers and social events.

The meeting began on Saturday with workshops on Modeling and Refinement of Nanoparticle Structures from Diffraction Data, Crystallography - World of Wonders, Refmac and Coot, and Structure Refinement and Disorder Modeling with OLEX2 on Saturday.

ACA Awards

[Daniel Nocera] Elizabeth Wood Writing Award winner Daniel Nocera (right) with John Spence at the Awards banquet. (Photo by P. Mueller.)

Five ACA awards were presented at this meeting. The Buerger Award to John Spence, the Warren Award to Paul Fenter, the Etter Early Career Award to Emmanuel Skordalakes, the Supper Instrumentation Award to Ron Hamlin, and the Elizabeth Wood Writing Award to Daniel Nocera.

[John Spence] John Spence during his Buerger Award lecture. (Photo by P. Mueller.)

In his Buerger Award lecture The Future of Diffraction Physics in Crystallography, John Spence noted that due to advances in instrumentation, crystallography continues to have a bright future. He focused upon two discoveries of the last decade - lensless imaging, pioneered in Janos Kirz's group, and the diffract-before-destroy approach to outrunning radiation damage, first suggested by Solem and demonstrated at Flash (the former Tesla Test Facility) in 2006. He reported the newest results from femtosecond diffraction experiments at XFEL. With lensless imaging, using oversampled diffraction data, electron-density maps from single particles can now be reconstructed. The group at the LCLS in Stanford has published several milestone papers using the diffract-and-destroy method of serial femtosecond crystallography (SFX). Pulses of X-rays, brief enough to outrun the resolution limiting effects of damage, are generated in a micron-sized beam from high-energy electron bunches with frequency 120 Hz and about 1012 hard X-ray photons per pulse. A constantly refreshed supply of protein nanocrystals flows across the beam in random orientations. By using short pulses instead of freezing, data can be collected at room temperature for many proteins which fail to grow crystals large enough for conventional macromolecular crystallography. Instrumentation has been developed by the ASU group (Doak, Weierstall, Fromme, Spence), the Monte-Carlo method for merging data from size-varying nanocrystals was described in the dissertation of Rick Kirian, and software was developed by Tom White in the DESY group. SFX milestones include the achievement of atomic resolution, and new biology elucidated by images of a drug target. Spence concluded with a review of the rich opportunities for new experiments in time-resolved structural biology at XFELS, including pump-probe experiments, new solutions to the phase problem and snap-shot biochemical dynamics, using correlated fluctuations in two-dimensional fast WAX patterns. These will be explored at a Royal Society Workshop on Biology with XFELS in October 2013.

Marius Schmidt
 
[Paul Fenter] George Phillips on the right, presenting the Warren Award to Paul Fenter. (Photo by P. Mueller.)
[XRIM] The X-ray reflection interface microscope (XRIM) images elementary topography on a solid surface through the use of phase contrast. The dark lines on the XRIM image correspond to 0.65 nm high steps, whose structure is shown (right).

Paul Fenter (ANL), winner of the 2012 ACA Warren Award, described his research on liquid-solid interfaces and their importance to energy-related processes critical to society. The B. E. Warren award is given to recognize an important recent contribution to the physics of solids or liquids. Because liquid-solid interfaces are buried beneath a liquid layer that is opaque to surface-sensitive structural tools, Paul and his colleagues developed phase-sensitive X-ray based scattering techniques to image structures at liquid-solid interfaces. He cited three examples: imaging of mineral-water interfaces and element-specific ion distributions at charged interfaces, and direct imaging of sub-nm lateral topography and structural variations.

Connie Rajnak
[Emmanuel Skordalakes] Emmanuel Skordalakes, at left, accepting the Etter Early Career Award from Eric Montemayor. (Photo by P. Mueller.)

The 2012 Margaret C. Etter Early Career Award was presented to Emmanuel Skordalakes (Wistar Inst., U. of Pennsylvania) for his elucidation of structure of telomerase, an RNA-dependent DNA polymerase that stabilizes chromosomes and is commonly over-expressed in age-associated disorders. Emmanuel presented structures of telomerase, alone and in complex with cognate RNA and DNA substrates. He and his colleagues tested hypotheses about telomerase function with a series of experiments inspired by the structures. His findings set the stage for the design of better therapeutics for treating diseases associated with aberrant telomerase activity

Eric Montemayor
[Ron Hamlin] Ron Hamlin on the left accepting the Charles Supper Award from ACA President George Phillips. (Photo by P. Mueller.)

Ron Hamlin, Area Detector Systems Corporation, was honored with the Charles Supper Instrumentation Award for his work in advancing the development of X-ray area detectors. His talk 2-D X-ray detectors – What do we really want and how can we build it? covered the development of X-ray detectors from film to the modern array detectors used today. His PhD project, with N.-H. Xuong, led to the construction of the first multiwire area detector, which became a national resource. Ron discussed the pros and cons of optical film scanners, single-point scintillation counters, image-intensified television cameras, and two-dimensional gas-filled, image-plate, CCD and pixel-array detectors. He discussed the characteristics of the 'ideal' X-ray detector that Ron and others have long strived to achieve. Ron also told about the ups and downs he faced as a small-business owner striving to keep pace with rapidly developing technology. His is an inspiring story about how the interest of a scientist/entrepreneur 30 years ago ultimately had an enormous impact on science.

John Rose

Poster Prizes

[Yimin Mao] Yimin was so excited to hear his name announced (this was his very first ACA meeting) that he took the podium to tell everybody how happy he was. The audience gave him a big round of applause. (Photo by P. Mueller.)

Seven Pauling Poster Prizes ($200, banquet ticket and a copy of a Linus Pauling book) were awarded. The Herman R. Branson Pauling Prize, named for one of the first African American crystallographers, went to Amber Smith. The Muttaiya Sundaralingam Pauling Prize, recognizing Sunderalingam's ground-breaking research on nucleic acids, went to Tamaria Dewdney. The Louis Delbaere Pauling Prize, with Canadian sponsorship, for the best poster from a Canadian laboratory went to Kevin Kevin Leung. Three other Pauling prizes went to: N. Alicea-Velazquez, Y.-T. Lai and C. Boone. The IUCr Pauling Prize, online access to all IUCr journals for one year or a volume of the International Tables, went to Serah Kimani. The RCSB Protein Data Bank Prize was awarded to Sergei Kalynych with an Honorable Mention to Rebecca Goldstein. The 2012 Crystal Engineering Prize, sponsored by CrystEngComm published by the Royal Society of Chemistry, went to Bo Wang. The 2012 Journal of Chemical Crystallography Prize went to Steffen Bernard and his co-authors D. Akey, S. Li, D. Sherman and J. Smith. The reported study revealed the presence of crystals of the same protein-substrate complex with different space groups and identical unit cell constants. This crystallographic anomaly occurred because a translation of layers within the crystal altered symmetry operators while maintaining the unit-cell composition. Jennifer Wierman received an honorable mention. The 2012 Oxford Cryosystems Low Temperature Prize was awarded to Yimin Mao of Brookhaven National Laboratory and his co-workers, who developed a specialized slam-freezing apparatus with rapid thrusting of the sample against a liquid-nitrogen cooled copper mirror, allowing examination by grazing-incidence X-ray scattering.

Bill Ojala

Undergraduate Education

[Protein speakers] Speakers in the session Protein and Small Molecule Crystallography at Undergraduate Institutions. (l to r) Douglas Juers, Alexander Norquist, Carla Slebodnick, Roger Rowlett and Kraig Wheeler. Inset: Joe Tanski.

Undergraduate education was addressed at a lecture preceeding the opening night reception and a symposium on crystallographic research with undergraduates. E. Mazur (Harvard U.) described his interests, involvment and creative ideas in the realms of education, science policy, outreach and the public perception of science. He reminded the audience that we learn not from lectures, but after class through self-study and discussions with fellow students. Mazur advocates peer instruction that capitalizes on the idea that the student knows the difficulty in understanding a concept better than the instructor. In the peer instruction environment the students can discuss the concepts presented by the instructor. Further information on Eric's teaching innovations is available at http://mazur.harvard.edu. In a half-day session J. Tanski (Vassar College) described strategies for X-ray diffractometer acquisition at a predominantly undergraduate institution and a teaching module that exposes undergraduate students to small-molecule crystallography including publication. C. Slebodnick (Virginia Tech) described a summer undergraduate crystallography workshop covering theory and practical sessions. R. Rowlett (Colgate U.) created a protein crystallography laboratory with remote or onsite data collection, structure determination and refinement, and the development of fruitful collaborations. D. Juers (Whitman College) also emphasized protein crystallography at undergraduate institutions with crystallography-focused biochemistry course units and research projects. A. Norquist (Haverford College) described his undergraduate research program involving the synthesis and structural properties of chiral vanadium tellurites. He described best practices for including students in the research and how to succeed without in-house X-ray facilities. K. Wheeler (Eastern Illinois U.) related his strategy, pitfalls and ultimate success in securing NSF-MRI funding.

Bruce Foxman, Bruce Noll and David Rose, Roger Rowlett and Kraig Wheeler

Past Reflections and Future Directions: 100 Years of Diffraction

[100 years speakers] Speakers in Past Reflections and Future Directions: 100 Years of Diffraction (l to r): Christine Beavers, Louise Dawe, David Rae, Brian Toby, Curt Haltiwanger, Paul Swepston, Hilary Jenkins, Sue Byram and Jenny Glusker.

In her opening presentation J. Glusker (Fox Chase Cancer Centre) reflected on 100 years of structure determination and gracefully put our science in context for the next generation of crystallographers. S. Byram, (Bruker AXS) described the Evolution of Small Molecule Crystallographic Instrumentation with examples of hardware (and software) innovations by many major industrial contributors. B. Toby (ANL) forecast the future of service crystallography and offered practical suggestions for its survival. H. Jenkins (McMaster U.) described exciting new software for viewing data (MAX3D). P. Swepston (Rigaku Americas Corp.) talked about collaborations which could lead to great science. Especially challenging 'small molecules' and methods of refinement were discussed by C. Beavers (LBNL) and A. D. Rae (Australian National U.), respectively.

Louise Dawe and Curt Haltiwanger

Transactions Symposium honoring Bruce Foxman

[Transactions speakers] Transactions symposium speakers (l to r): Bruce Foxman, David Watkin, Graciela Diaz de Delgado, Kraig Wheeler, Roger Bishop, Magali Hickey, Richard Adams, Menahem Kaftory, Larry Falvello, Carolyn Brock, Michael Ward.
 
[Coppens figure] Top: Cu1 and Cu2 show the difference in packing of two independent molecules in crystals of a Cu(I) phenanthroline complex. Bottom: Time-resolved photodifference map showing that the structural changes on photoinduced electron transfer to the microsecond lifetime excited state are different. Red: positive. Blue: negative. Isosurfaces ±0.25 e/Å3. [J. Phys. Chem. A, 116, 3359-3365 (2012), and Acta Cryst. A67, 319-326 (2011).] (Philip Coppens)

Transformations and Structural Oddities in Molecular Crystals covered crystal transformations, supramolecular assemblies and synthesis, polymorphism, and function and reactivity of engineered materials. Talks were presented by Bruce's friends, colleagues and former students, who also held a birthday party for him and shared anecdotes that highlighted Bruce's impact on their careers. At the symposium D. Watkin (Cambridge U.) discussed systematic studies of Z′ > 1 structures, C. Brock (U. Kentucky) showed how optimizing hydrogen bonds within structures and using enantiomerically and diasteriomerically pure compounds can assist the formation of crystal structures with multiple molecules in the asymmetric unit. P. Coppens (SUNY Buffalo) discussed the use of dynamic photocrystallography to explore linkage isomerism and its application to stereoselective transformations of structures with Z′ = 2. K. Wheeler (Eastern Illinois U.) designs J-shaped molecules that form robust supramolecular dimers which undergo photodimerizations via single crystal-single crystal processes, often with quantitative conversions. J. Bernstein (NYU Abu Dhabi) described some interesting aspects of crystallographic history including the fact that Reginald James, a physicist on Shackleton's 1914 Antarctic expedition, later acquired a reputation as an authority in the newly developing field of crystallography. M. Kaftory (Technion-IIT) showed that UV illumination of a class of pyridines results in photodimerization in which reactants undergo molecular flips. M. Garcia-Garibay (UCLA) explained strategies for engineering reactions in crystals with examples of photodenitrogenation of diazo compounds, nitrenes and azoalkanes. V. Young (U. Minnesota) described an ionic salt that exhibits enantiotropic phase transitions. The system starts from a non-twinned crystal structure and progresses to lower symmetry accompanied by twinning and an order-disorder transition. The transition was followed with the Dynamic Compression Sector (DSC) and X-ray data. B. Kahr (NYU) related his recent adventures with molecular crystals that grow helically with twisted lattice planes. J. Swift (Georgetown U.) described the impact of growth conditions and dye additives on the formation of uric acid crystals. Ö. Almarsson (Alkermes) addressed the importance of crystal structure analysis and data mining for pharma R&D. M. Hickey (Alkermes) discussed optimizing pharmaceutical material performance, the impact of chemical changes on crystal structure and properties, and the use of crystallographic data to understand solid-state reactivity in drugs. M. Hollingsworth (Kansas State U.) showed that co-crystallization of urea with alkanes, alkanones and alkanediones generates ferroelectric domain-switching materials having twinning, phase transitions, and commensurate and incommensurate phases. M. Peterson (Amgen) described co-crystallization of urea with an α,ω-disubstituted hexane that produced stacked loops of ureas that form undulating channels. L. Falvello (U. Zaragoza) described his preparation of metal-citrate building blocks with a variety of cubane topologies and solid-state reactivity. The talk on iridium- and osmium-gold carbonyl clusters by R. Adams (U. South Carolina) drew attention to the complexities of CO labile systems. A. Rheingold (UCSD) showed that in mixed-valence iron acetates the rates of intramolecular electron exchange vary greatly, that local symmetry plays an important role in this phenomenon, and that it is solvent-dependent. G. Diaz de Delgado (U. de Los Andes) described the sources of complex structural features of metal carboxylates. R. Bishop (U. New South Wales) addressed supramolecular synthesis, the structural preferences of molecular tweezers, and the inverse relationship between clathrate formation and packing prediction. M. Ward (NYU) discussed assemblies of his guanidinium organosulfonate building blocks, with remarkable properties including soft matter microstructures that mimic Archimedean polyhedra. K. Harris (Cardiff U.) described the use of solid-state NMR to monitor the evolution of supramolecular assemblies as a function of time.

Graciela Diaz de Delgado, Magali Hickey and Kraig Wheeler

Emerging Sources: Theory and Practice

[Emerging sources speakers] Speakers in Emerging Sources: Theory and Practice (l to r): back, Henrik Lemke, Marius Schmidt, Yun-Xing Wang. In front: John Tainer, Dilano Saldin, Friedrich Schotte, Marc Messerschmidt, Peter Schwander.
 
[Saldin figure] 3D images of the icosahedral satellite tobacco mosaic virus (STNV) reconstructed from simulated diffraction patterns from random orientations of the virus as expected from proposed 'diffraction-before-destruction' experiments with an X-ray free-electron laser (XFEL). The image shows a computational slice through the image, revealing the hollow character of the protein capsid whose atomic coordinates from the PDB were assumed in the simulations of the diffraction patterns. D. K. Saldin et al., Optics Express, 19, 17318-17335 (2011).

In the first of three sessions on Emerging Sources: Theory and Practice, J. Tainer (Scripps Inst.) discussed small- and wide-angle X-ray scattering (SAXS/WAXS) techniques, introduced the BioISIS data base as a resource for macromolecular SAXS, and predicted that time-resolved SAXS with millisecond time-resolution will soon become routine. F. Schotte (NIH) illustrated pico-second time-resolved synchrotron experiments with a movie of structural changes immediately after carbon monoxide was flashed away from the heme-iron position in carbonmonoxy-myoglobin. P. Schwander (U. Wisconsin), a major developer of embedding diffraction data into low-dimensional manifolds, demonstrated how manifold embedding allows one to study structural heterogeneity and removes the need for identical molecules. He showed that manifold embedding faithfully separates unlike particles at the experimental signal-to-noise ratio of cryo-EM. D. Saldin (U. Wisconsin) demonstrated how to determine the structure of viruses from diffraction patterns of random orientation without crystals by averaging the angular correlations of a large number of diffraction patterns from an ensemble of identical objects. Such diffraction patterns could be obtained using the ultra-short X-ray pulses available at the XFEL. P. Musumeci (UCLA) described the Pegasus, a source of relativistic electrons for ultrafast time-resolved electron diffraction experiments with high spatial and temporal resolution. The time-resolved melting of gold particles was given as an example. U. Weierstall (Arizona State U.) concentrated on injector technology used to perform recent experiments at LCLS. He outlined some advantages of serial nanocrystallography: nanocrystals are readily obtainable, allow dynamic processes to be followed and scatter intensity between the Bragg positions, which can be used to solve the phase problem. The small crystals are injected into the beam by a liquid jet whose diameter and velocity can be controlled by a surrounding gas stream. He described an international collaboration on nano-sized crystals of lysozyme and photosystem.

I. Marius Schmidt and Yun-Xing Wang

The second session, focused on SAS, was dedicated to the memory of Hiro Tsuruta, a pioneer in the field. P. Pernot (ESRF) described BM29, an instrument optimized to measure hundreds of protein solution samples quickly without user intervention. T. Weiss (SSRL,) described BM4-2, an instrument capable of accommodating static and time-resolved experiments on proteins in solution and lipid membrane structures. L. Yang (NSLS) described the nearly completed LiX beamline which will permit time-resolved solution scattering using continuous flow cells, scattering-based scanning-probe tissue imaging, and scattering from membrane proteins embedded in single-layered lipid membranes. S. V. Pingali (ORNL) described Bio-SANS, the only facility in the world specifically dedicated to biological applications of small-angle neutron scattering (SANS). The instrument is operated by the Center for Structural Molecular Biology (CSMB) at the High Flux Isotope Reactor of ORNL. W. Heller (ORNL) described the Extended Q-Range Time-of-Flight SANS instrument that possesses a large dynamic measurement range at a single configuration and a high available flux suitable for weakly scattering samples and kinetics studies. J. Barker (NIST) reported on the very small-angle neutron scattering (vSANS) diffractometer, currently under construction at NIST.

Volker Urban and Lin Yang

In the third SAS session, T. Graber and Z. Ren (BioCARS) contrasted the properties of third-generation sources such as the APS with those of spectacular new X-ray free-electron (XFEL) sources such as the Linac Coherent Light Source at Stanford. Third-generation sources offer ready accessibility to users, pink or monochromatic X-rays, high stability, a very high rep rate, and mature beamline instrumentation and experimental design, but cannot come close to XFELs in photons per pulse or brevity of their pulses. However, Ren described pump-probe experiments which offer a time resolution less than the X-ray pulse length. By systematically tracking the laser pulse across the X-ray pulse, the length of the trailing period is smoothly varied. Ren showed, in initial time-resolved crystallographic experiments, that this conceptually simple general approach, 'poor man's pulse slicing', can yield a time resolution <100 ps. These experiments require a systematic study of the photophysics to achieve maximum yield of the desired species. J. van Thor (Imperial College London) described such a laser-lab-based study of the photocycle of photoactive yellow protein using fs laser pulses. The yield depends on pulse wavelength, intensity and duration, and on whether or not the pulse is chirped. Macromolecular crystallography increasingly focuses on tiny crystals, which requires the design and implementation of purpose-built beamlines that offer a tightly-focused X-ray beam, low X-ray background, the ability to visualize and center tiny crystals, and precision in crystal goniometry to ensure that the crystal remains centered in the beam. M. Yamamoto (Spring-8, Japan) described a new beamline at Spring-8 that has these characteristics. W. Kong (Oregon State U.) described a radically new, laboratory-based approach to structure determination of single proteins based on the incorporation of proteins into superfluid helium droplets at 0.38 K without significant unfolding. An elliptically polarized laser beam is used to orient the droplets and the electrons are scattered by the now-oriented protein molecules. The goal is to generate a complete three-dimensional electron-scattering pattern from which the structure could be reconstructed. This overall approach is technically challenging, and Kong presented results on successful initial steps in this high-risk high-reward project.

Keith Moffat

Extended Wavelength X-ray Crystallography

[Extended wavelength speakers] Speakers in Extended Wavelength X-ray Crystallography (l to r): Meitian Wang, Robert Fischetti, Jim Pflugrath, Armin Wagner, Christoph Mueller-Dieckmann, Matthew Benning, B.C. Wang, Manfred Weiss, Naohiro Matsugaki, Wayne Hendrickson and Zhi-Jie Liu.

The session focused on the use of extended-wavelength X-rays (0.7 Å to 3.5 Å and above) in structural biology, addressing new beamlines and equipment, sulfur phasing, phosphorous phasing and halide phasing. B.-C. Wang (U. Georgia/SERCAT/APS) described successful S-SAD phasing from a single insulin crystal with reduced radiation dose using a multiple-data-set (MDS) collection approach. He showed that the oxidation states of metals/ions could be monitored using data collected across the Fe absorption edge for crystals of bovine catalase. C. Mueller-Dieckmann (ESRF) described recent upgrades and plans to maximize the success of macromolecular crystallography experiments with the addition of the MASSIF sample-evaluation and sorting facility and upgrades to ID29 to collect data with low energy (E = 5 keV, λ = 2.5 Å) X-rays. He also described methods of soft X-ray data collection including cluster analysis. N. Matsugaki (Photon Factory) described a beamline dedicated to SAD/MAD experiments that uses wavelengths greater than 2.7 Å to enhance weak anomalous signals. The beamline has loopless 'capillary-top mounting' to reduce the background noise. Naohiro described recent sulfur-SAD phasing of the 2.5 Å structure of a 43 kDa glucose isomerase for which automated model building was able to fit nearly all of the residues. J. Pflugrath (Rigaku, USA) illustrated the simplicity of using of halide (KI) soaks for SAD phasing with a video entitled 'Mastering the Halide Swish' produced by his colleagues S. Lee and J. Rieger. He stressed that highly redundant data is not essential for successful SAD phasing. M. Benning (Bruker AXS) presented statistics (year, resolution and solvent content) on in-house SAD phased structures in the PDB, emphasized the importance of data optimization and presented successful results from crystals of moderate diffraction quality using S-SAD phasing. He noted that although his data sets were low-resolution they had high redundancy and one case required two crystals. He reported the successful phasing of a 42 kD protein soaked with PtCl4. M. Weiss (Helmholtz-Zentrum Berlin) discussed challenges and problems in using long-wavelength X-rays. He noted that over 50 methodological papers have been published and presented the statistics of S-SAD structures (wavelength, amino acids per asymmetric unit and symmetry group). He gave details of three determinations, suggested ways to improve the success of S-SAD phasing, considering crystal mounting, data collection and data processing, and noted that based on the ratio of amino acid content to sulfur atoms more than 96% of all proteins could be possible targets for S-SAD phasing. A. Wagner (Diamond Light Source) emphasized that Beamline I23 will be the first MX beamline optimized for the long-wavelength region (1.5-4 Å). He showed that the optimal wavelength for S-SAD is 4.5 Å for 0.05 mm sized crystals and 3.4 Å for 0.1 mm sized crystals. To minimize absorption effects, the complete beamline including sample, goniometer and detector will be operated in a vacuum. An X-ray tomography setup will be used for analytical absorption corrections. Sample cooling will be achieved using a conductive path running from a pulse tube cryo-cooler through the κ goniometer. A large curved detector will allow access to diffraction data up to 2θ = ±90°. M. Wang (Swiss Light Source) described improving the signal to noise ratio in S-SAD and P-SAD phasing experiments using the X06DA super-bending magnet beamline which has a double channel-cut monochromator, PRIGo multi-axis goniometer and new PILATUS 2M detector. The PRIGo goniometer is able to place the best part of the crystal in the beam, align long crystal axes to avoid overlaps, record Bijvoet pairs on the same image and carry out multi-pass data collection with different crystal orientations. Meitian presented stuctures determined with data from the new system of an RNA 14mer, the sarcin/ricin loop and three S-SAD proteins with amino acid lengths ranging from 84 to 387. Z.-J. Liu (Inst. of Biophysics, Beijing) described new tools for S-SAD phasing including X2DF, an updated version of the SCA2 system, and illustrated the use of X2DF in the structure determination of a 40 kD protein. W. A. Hendrickson (Columbia U., NSL) reported using cluster analysis to merge S-SAD data sets collected from multiple crystals. Five examples discussed ranged from 22 to 1200 residues per asymmetric unit with resolutions ranging from 2.8 Å to 2.3 Å. The elemental identities for Ca, Cl, S, P and Mg associated with the structures were confirmed by f′′ scattering factor refinement using PHENIX. The procedures used in the analysis are robust and when aided by synchrotron beamlines optimized for low-energy X-ray diffraction measurements will offer truly routine structure determination of native macromolecules.

Bi-Cheng Wang and Robert Fischetti

Advanced Hardware and Applications

[Hardware speakers] Speakers in Advanced Hardware and Applications (l to r): Malcolm Capel, John Rose, Howard Robinson, Michael Blum, Aina Cohen, Christian Brönnimann, Sandro Waltersperger, David Schuller. (Ron Hamlin not pictured)

The session focused on recent advances in X-ray area-detector technology, robotics and automated data being incorporated at beamlines in the US and elsewhere. H. Robinson described the Qmx data-collection system developed at NSLS. S. Waltersperger (Swiss Light Source) described the PRIGo multi-axis goniometer recently installed on beamline X06DA and D. Schuller (CHESS) gave an update on the installation of the second-generation Berkeley Automounter (BAM-2) at MacCHESS. A. Cohen (SSRL) conducted a live demo of a remote-access in situ UV-visible absorption spectroscopy system to monitor metal oxidation states within protein crystals. C. Brönnimann (Dectris Ltd) described developments related to their PILATUS photon-counting detector, M. Capel (NE-CAT/Cornell U.) reported on the PILATUS 6MF pixel-array detector installed on NE-CAT's undulator beamline 24-IDC, M. Blum (Rayonix LLC) described a new generation of detectors based on Split Frame Transfer CCDs, J. Rose (SER-CAT/U. of Georgia) presented plans for integrating the fast Rayonix MX300HS detector into the SER-CAT beamline 22ID, and R. Hamlin (Area Detector Systems Corporation) described a new type of pixel-array detector called the Dual Mode Pixel Array Detector (DMPAD) that ADSC is developing which addresses the problem of co-incidence loss common to PAD detectors at high count rates. In related posters, D. Szebenyi (CHESS) described high-pressure cryocooling, J. Jenkins (TTP Labtech Ltd) reported on an automated gradient maker designed to rapidly generate screening or optimization crystallization plates, T. Allison (Labcyte Inc) described the Echo liquid handler that can transfer nanoliter quantities of reagents including viscous and osmotic fluids, and A. Gonzalez discussed the 'AutoDrug' pipeline developed at SSRL.

John P. Rose and John Chrzas

Public Domain Software

[Software speakers] Speakers in Public Domain Software (l to r): Xiaoping Wang, Richard Cooper, George Sheldrick, Anthony Spek, Ronan Keegan, Robert Von Dreele, Oleg Dolomanov, Nicholas Sauter.
 
[CRYSTALS figure] Disorder modeling in CRYSTALS.

A. Spek (Utrecht U.) presented the latest developments in PLATON. Many changes for CIF Validation, SQUEEZE, TwinRotMat and Bijvoet analysis tools were implemented in the new SHELXL-2012. PLATON is available online at www.cryst.chem.uu.nl/spek/platon/. R. Von Dreele (ANL) presented The General Structure Analysis System II (GSAS-II), which has been rewritten in Python. It is available for Windows, Linux and Mac OSX platforms and is now loaded with graphics and mathematical packages. GSAS-II has visualization tools for single-crystal, powder, texture and PDF analysis. Currently, GSAS-II handles only monochromatic CW X-ray/neutron data for powder, single-crystal and PDF applications. The program has yet to be developed for neutron time-of-flight data, which was a distinctive capability of the original GSAS program. GSAS-II is available online at https://subversion.xor.aps.anl.gov/trac/pyGSAS. O. Dolomanov (OlexSys Ltd, UK) presented the newest version of Olex2, an open-source project originated at Durham U. that combines crystallographic packages for small-molecule structure solution and refinement with a single easy-to-use interface that is available online at www.olex2.org. G. M. Sheldrick (U. Göttingen) presented his new SHELXL-2012 open-source program that has been tested by 100 beta-testers. Precompiled binaries for Windows, Linux and Mac platforms are available to download. SHELXL-2012 includes many new features for modeling disorder, generating non-classical C-H⋯O hydrogen bonds and extending rigid-bond restraints. Improvements in data-collection hardware and software now make it possible to determine absolute structure even when the anomalous scattering is extremely weak. For non-centrosymmetric structures SHELXL-2012 calculates the Flack parameter at the end of the refinement by two different methods. The hkl data and the .res file from the final structure refinement are now embedded into the .cif output file with checksums included. This makes it possible to repeat any refinement exactly, and discourages cosmetic editing of the CIF file. More information at shelx.uni-ac.gwdg.de/SHELX/. CRYSTALS has been maintained in the Chemical Crystallography Laboratory in Oxford for 40 years. It is an X-ray and neutron crystal structure refinement package widely used in research, teaching and service. R. I. Cooper (Oxford U.) presented new features of parallel computation, asymmetric restraints and tools for modelling disorder in CRYSTALS (www.xtl.ox.ac.uk/crystals.html).

R. Keegan (CCP4) introduced AMPLE, an automated software tool jointly developed by the U. of Liverpool and CCP4 for protein structure solution with the employment of ab initio protein structure modeling techniques in molecular replacement. Structures of smaller proteins or protein domains can now be reliably predicted for use as search models in cases where no homologous structure is available. AMPLE is designed to make this technique available to users in an automated way that requires only limited computational hardware resources. Initial tests on a set of 296 cases drawn from the PDB showed that the techniques employed in AMPLE can result in solutions for approximately 40% of the targets. A beta release version is included in the latest release of the CCP4 software suite: www.ccp4.ac.uk. New efficient software tools are needed for high-throughput work in data processing as light sources and detectors continue to improve. N. Sauter (LBNL) demonstrated a Python-based software tool that provides a flexible platform for addressing these issues. The current BPCX package contains a Python-based image viewer and a still-image data-reduction toolbox, cctbx.xfel, capable of handling concurrent event requests with the use of a multiprocessing server, cctbx.so.

Xiaoping Wang

Radiation Damage

[Damage speakers] Speakers in Radiation Damage (l to r) back: Robert Thorne, James Holton and Graeme Winter; front: Ana Gonzalez, Stephan Ginell, Zou Finfrock, Elspeth Garman and Sandor Brockhauser.

The speakers in a session on Radiation Damage addressed different aspects of the phenomenon, including how to measure and minimize it (J. Holton, BMB/PBD, U. C. San Francisco, and E. Garman, U. of Oxford), temperature and time dependence of it (R. Thorne, Cornell U.), spatial dependence and penetration depth of photoelectrons (Z. Finfrock, U. Washington), and modeling how to live with it (S. Brockhauser, EMBL-Grenoble, and G. Winter, Diamond Light Source). To minimize damage, Garman recommended back-soaking non-specifically bound heavier atoms out of crystals to reduce the absorbed dose per incident photon, matching beam size to crystal size, using a 'top-hat' shaped beam if possible, and making sure the beamline yielded enough information to estimate the dose for your experiment to determine what your crystals would tolerate. Thorne reported that by collecting data in ∼1 ms, using dose rates which approach 1 megagray per second and a fast detector, approximately half of the radiation damage near room temperature could be outrun.

Stephan Ginell and Ana Gonzales

General Interest

[General speakers 1] Speakers in General Interest I: (l to r) back: Allen Oliver, Ethan Merritt, Edwin Pozharski and Bernhard Rupp; front: Lee Daniels, Mathias Meyer and Charles Campana.
[General speakers 2] Speakers in General Interest II (l to r) back: Allen Oliver, Alexander Merriman, Renping Qiao and Christopher Dettmar; front: Pranoti Navare, Constance Jeffery and Karim Sutton.

The first of two sessions organized by the General Interest SIG drew a packed house as speakers addressed the scandals surrounding fabrication of crystallographic data. E. Pozharski (U. Maryland) and B. Rupp (Hofkristallamt) provided examples of structural analyses that were either unintentionally in error or deliberately fabricated. They presented troubling and inconsistent characteristics in published data. The take-home message: it is easier to produce a genuine crystal structure than a fabrication. Reviewers, authors and readers need to be vigilant. E. Merritt (U. Washington) presented a methodology for translation, libration and screw analysis of molecular motion that reveals the quality of a structure determination. C. Campana (Bruker), Lee Daniels (Rigaku) and M. Meyer (Agilent Technologies) discussed the merits of current hardware and software available for chemical crystallography. C. Dettmar (Purdue U.) discussed particle size analysis and ways to prepare amorphous samples using fluorescence. P. Navare (Worcester Polytech) demonstrated how enantioselectivity can be induced on solid surfaces by appending chiral SAMs (self-assembled molecules) to the surface of the substrate. C. Hu (NYU) described the complexity of in situ crystal-to-crystal transformations of glycine. Etter Student Lecturer K. Sutton (Oxford, UK) demonstrated how a tunable source can be used to calculate populations of differing oxidation states of an element. This technique could be useful for structures in which doping or partial oxidation of an element as a charge carrier (semiconductors, super conductors) is present. C. Jeffery (U. Illinois at Chicago) discussed 'moonlighting' proteins that have two distinctly different functions that are present in many species. M. Matho (La Jolla Inst. for Allergy and Immunology) discussed the virus envelope protein D8 and how its study may contribute to developing vaccines. R. Qiao (Max Perutz Labs, Austria) described a membrane protein that simultaneously opens channels and provides rigidity. The final speaker, high-school student A. Merriman (HWI), described using conserved three-dimensional folds and amino acid sequences of ribosomal proteins to determine a rooted phylogenic tree of all species.

Allen Oliver

In Situ Parametric Studies

[In situ speakers] Speakers in In Situ Parametric Studies (l to r): Antonio dos Santos, Scott Misture, Kamila Wiaderek, Garrett Granroth, Dermot O'Hare, Mario Wriedt and Peter Khalifah; inset: Xiang-Quiang Chu.

At the Diamond Light Source in the UK, D. O'Hare (Oxford U.) used a custom-built cell for the in situ study of the flux growth of Bi5Ti3Fe(1-x)MnxO15. M. Wriedt (Texas A&M) presented his study of a copper-based metal-organic framework material in which a single reaction led to the formation of three different crystals having different hydration states and magnetic properties. The hydration state was reversibly controlled in situ by temperature and humidity. At the Sequoia time-of-flight spectrometer at the Spallation Neutron Source, G. Granroth (ORNL) described a study that clarified details of two of the high-field magnetic structures of MnWO4 which has at least 6 phases. S. Misture (Alfred U.) measured electrochemical properties of transition metal oxides using high-temperature data collected under a controlled atmosphere. The in situ electrochemical activity was related to the phases present under experimental conditions, mimicking the operational environment of fuel cells. P. Khalifah (SUNY Stony Brook) described de-lithiation paths and degradation of LiFeBO3, a high-capacity battery material.

K. Wiaderek (ANL) studied the structure and size of nanoparticles in iron-based battery materials under operational conditions in a custom-made electrochemical cell on both nano- and meso-scales. X.-Q. Chu (ORNL) discussed the use of quasi-elastic neutron scattering to study the relaxational dynamics of lysozyme and an inorganic pyrophosphatase. The slow dynamics of these globular proteins could be adequately modeled by the mode-coupling theory.

Antonio dos Santos

Magnetic Materials

[Magnetic speakers] Speakers in Magnetic Materials (l to r): Ovidiu Garlea, Ashfia Huq, Susan Herringer, Simon Parsons, Timothy Munsie, John Greedan and Dimitry Khalyavin.

This session featured materials synthesis, molecular magnets studied under pressure and three different families of compounds which have exciting magnetic properties. J. Greedan (McMaster U.) discussed short- and long-range magnetic order observed in vacancy ordered/disordered perovskite structures. D. Khalyavin (ISIS, Rutherford Appleton Laboratory) introduced the hexagonal lattice system RBaCo4O7 where a new exchange topology exhibiting geometrical frustration gives rise to varied degrees of spin correlation. O. Garlea (ORNL) described the effect of oxygen doping on the structural and magnetic properties of delafossite compounds. The second half of the session included studies of molecular based magnets under pressure, effects of random exchange in ferromagnetic copper chloride chains and studies of single-crystal holmium titanate.

Ashfia Huq

To be continued in the next issue.