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Douglas (Doug) Dorset (1942-2016)

We are sad to announce that Dr Douglas Dorset passed away on 8 December 2016.

Douglas Dorset's career as an electron crystallographer started when he joined Dr Donald Parson's electron-crystallography laboratory at Roswell Park Cancer Institute in 1971. In 1973 he moved to the Medical Foundation of Buffalo - now the Hauptman-Woodward Medical Research Institute - where he headed the Electron Diffraction Department and did the fundamental work for which he is best known. Douglas moved to ExxonMobil Research and Engineering Company in 2000, investigating the structure of wax crystals and how these change in the presence of modifiers. His research encompassed new methods and an array of crystallographic studies on zeolites, polyolefins and other materials.

In the face of those who said that electron-diffraction data could not yield quantitative results, he argued long and hard that the problem of dynamical scattering could be overcome and that electron-diffraction data could yield ab initio structure determinations. He was responsible for bringing the work on electron crystallography of Vainshtein and Zvyagin in Moscow to the attention of a larger western audience. He developed techniques to overcome the problems of the missing cone of data, dynamical scattering, radiation damage and sample problems. His breadth of applications included polymers, waxes, zeolites, fibers, cholesterol derivatives, fullerenes, phthalocyanines, solid solutions of paraffins and proteins at low resolution.

Douglas received the A. L. Patterson Award in 2002 from the American Crystallographic Association. He was within the top 1% of most-cited authors in the chemical literature, worldwide, 1981-1997 (compilation of David A. Pendlebury, Institute for Scientific Information). He was a member of the IUCr Commission on Electron Diffraction (now Electron Crystallography) from 1993 to 2002 (Chair 1999-2003), and a Co-editor of Acta Crystallographica Section A from 1999 to 2011. He was on the Editorial Board of the Journal of Electron Microscopy Technique (1988-2010) and Associate Editor of Microscopy Society of America Bulletin from 1992 to 1994.

Douglas was involved in organizing several of the IUCr International Schools of Crystallography in Erice, Sicily, as well as many other schools on crystallography around the world and numerous sessions at major national and international meetings. He was a good teacher and co-supervised research students in several countries, an enthusiastic supporter of many young researchers - who are now active electron crystallographers. Douglas always had time to discuss the finer points of an analysis, or to mentor others in need of some inspiration. He encouraged many of us in our work during the early years of electron crystallography, when its power was not fully embraced by the global crystallography community. His impressive knowledge of all aspects of crystallography will be remembered by all who met him.

Lisa Baugh, Mark Disko, William Lamberti, Karl Strohmaier, William Duax, John Fryer, Sven Hovmöller, Xiaodong Zou, Laurence Marks and Stavros Nicolopoulos

research news

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A step to understanding polymorphs

In a paper published in Acta Cryst. B, (2016), doi: 10.1107/S2052520616017297  Carol Brock of the University of Kentucky looks at some of the organizing principles behind crystal structures with high Z’, where Z’ is loosely the number of symmetry-independent molecules in the asymmetric unit. This study lies at the very heart of understanding and being able to control properties of molecular structures. Pharma and agrichem industries attach great importance to understanding crystal structure. The solid form impinges directly on properties such as solubility, bioavailability, processing characteristics, bulk density, dissolution rate, permeability, surface electrostatic charge and so on, so it is imperative to have a clear understanding of the molecular-level make-up of a material and how this affects its properties. This study illustrates that the high Z’ phenomenon, like polymorphism itself, has many root causes but careful study of each structure allows the identification of organization principles in most cases.

Brock leaves the door open for future research saying “very few structures are so complex that it is difficult to understand how the crystals could have formed”. This comprehensive survey, in conjunction with a groundswell of work by a number of groups on this increasingly intriguing problem over the past 20 years, shows that there is no one-size-fits-all explanation and that the details of each structure are uniquely tied to the chemical details of the molecules that comprise it. The search goes on, but perhaps we are now at least beginning to know how to formulate the question.

Taken from a commentary written by Jonathan W. Steed and published in the journal Acta Cryst B.

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Quantifying radiation damage in SAXS experiments

Biological small-angle X-ray scattering (SAXS) is an experimental technique that provides low-resolution structural information on macromolecules. The surge of popularity of the technique is a result of recent improvements in both software and hardware, allowing for high-throughput data collection and analysis, reflected in the increasing number of dedicated SAXS beamlines such as BM29 at the ESRF, P12 at EMBL Hamburg and B21 at Diamond Light Source.

However, as for most other macromolecular structural techniques, radiation damage is still a major factor hindering the success of experiments. The high solvent proportion of biological SAXS samples means that hydroxyl, hydroperoxyl radicals and hydrated electrons are produced in abundance by the radiolysis of water when it is irradiated with X-rays. These radicals can then interact with the protein molecules, ultimately leading to protein aggregation, fragmentation or unfolding. Furthermore, molecular repulsion due to protein charging can also decrease the scattering at low angles.

Common methods used to reduce radiation damage to biological SAXS samples are generally concerned with limiting the X-ray exposure to any given volume of sample. In an analogous manner, cryo-cooling samples down to 100 K for SAXS (cryoSAXS) has been reported to increase the dose tolerance of SAXS samples by at least two orders of magnitude.

Applications of the above radiation damage mitigation approaches are unable to completely circumvent its detrimental effects, in particular the change of the scattering profile throughout the experiment. It is necessary to determine whether any two scattering profiles are similar so that noise can be reduced by averaging over similar curves.

For experiments by different researchers to be inter-comparable, the progression of radiation damage is most usefully tracked as a function of the dose absorbed by the sample. RADDOSE-3D is a free and open source software program used to calculate the time- and space-resolved three-dimensional distribution of the dose absorbed by a protein crystal in a macromolecular crystallography experiment; however, there is no equivalent software available for SAXS. Radiation damage studies in SAXS thus currently require the experimenters to correctly parameterize the experiment and manually calculate a single estimate of the dose within the sample.

In a paper published by Brooks-Bartlett et al. [(2017), J. Synchrotron. Rad. 24, doi:101107/S1600577516015083], extensions to RADDOSE-3D are presented, which enable the convenient calculation of doses for SAXS experiments, reducing the burden of manually performing the calculation. Additionally, the authors have created a visualisation package to assess the similarity of SAXS frames and used these tools to assess the efficacy of various radioprotectant compounds for increasing the radiation tolerance of the glucose isomerase protein sample.

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Microseeding: a new way to overcome hemihedral twinning?

Twinning is a crystal-growth disorder in which the specimen is composed of distinct domains whose orientations differ but are related in a particular, well-defined way. Twinning, which is a known problem in protein crystallography, usually hampers high-quality crystal structure determination unless it is detected and either avoided or corrected. Although effective computational methods have been developed for the determination of structures using data from twinned crystals (known as 'detwinning'), if possible it is preferable to obtain crystals that are not twinned.In some cases, optimising the length of the protein fragment used for crystallisation can lead to the growth of untwinned crystals, but this is a time-consuming process.

In a recent paper in Acta Crystallographica Section F, microseeding was used to produce untwinned crystals of LigM, an O-demethylase from Sphingobium sp. SYK-6, using twinned crystals as seeds. Microseeding is one of several seeding techniques that are used to successfully separate nucleation events from crystal-growth events. In this technique, crystals are used as seeds and introduced into new drops which are equilibrated at lower levels of supersaturation. It has frequently been used to improve reproducibility in crystallization and can yield different crystal forms.

In the work described by Harada et al. [(2016). Acta Cryst. F72, 897-902; doi:10.1107/S2053230X16018665], around 50% of the initially obtained crystals of LigM were hemihedrally twinned. These crystals were then used as a seed stock for microseeding. In combination with optimization of the reservoir solution, this led to crystals that were not twinned and belonged to a different space group. It is hoped that this method will have potential as a more general simple method for overcoming hemihedral twinning in protein crystals.

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Why keep the raw data?

The increasingly popular subject of raw diffraction data deposition is examined in a Topical Review in IUCrJ [Kroon-Batenburg, Helliwell, McMahon & Terwilliger (2017). IUCrJ, 4, doi:10.1107/S2052252516018315]. Building on the 2015 workshop organised by the IUCr Diffraction Data Deposition Working Group (DDDWG), the authors bring the story up to date with accounts of new subject-specific and institutional data repositories, and of growing policy pressures on research data management such as the European Open Science initiative.

The article is, however, more than just a workshop report or a survey of evolving policy. It seeks to inform the cost-benefit arguments over diffraction data deposition with examples from real front-line research. For example, Kroon-Batenburg and Helliwell have collaborated on studies of protein binding of the chemotherapeutic agent cisplatin, and have made all their 34 raw data sets available through the University of Manchester Data Library. Some of these datasets have been reanalysed and resulted in fresh understanding of cisplatin-lysozyme models.

The prospect of extracting further information from archived primary data sets in this way (either by the insights of fresh pairs of eyes or through subsequent improvements in software analysis) has implications for structural databases, facilitating the idea of continuous improvement of studies, such as for macromolecular structure models (long championed by Terwilliger).

It is not only in the field of macromolecular structure determination that these considerations are important. One of the greatest challenges to reusing any raw data is the need for complete metadata associated with any raw data set, to allow its subsequent interpretation and full evaluation.

Various IUCr Commissions are actively publishing their summaries of the essential metadata that need to be captured alongside all experimental data sets. These initiatives and their relationship to the IUCr's standard for data characterization (CIF, the Crystallographic Information Framework) are reviewed within the article. Again, practical pointers are given to essential metadata that need to be captured alongside diffraction data sets.

While there are encouraging signs that the scientific community is taking more informed interest in data management and its scientific potential, fresh challenges are being thrown up by the latest generation of instrumentation, capable of generating vast amounts of data at an incredible rate. It may not be possible to archive or even thoroughly analyse all the data that is being produced. However, this article will help to supply a deep understanding of the reasons why society should invest effort and resources into extracting the greatest value possible from the data deluge, in crystallography as in any science.

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The coming of age of macromolecular neutron crystallography

The protein crystallography station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for thirteen years. The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualisation of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. A review article published by Chen and Unkefer [(2016). IUCrJ. 4, doi:10.1107/S205225251601664X], highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

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