|The IUCr is an International Scientific Union. Its objectives are to promote international cooperation in crystallography and to contribute to all aspects of crystallography, to promote international publication of crystallographic research, to facilitate standardization of methods, units, nomenclatures and symbols, and to form a focus for the relations of crystallography to other sciences.|
IUCrJ, the only journal to carry the name of the International Union of Crystallography, was launched in January 2014 with a simple mission: to attract high-quality science papers of broad scientific significance from across the full breadth of the scientific communities that use structural information.
We are pleased to announce the journal will start accepting articles in cryo-electron microscopy (cryoEM) within the Biology and Medicine section. CryoEM is proving to be a powerful tool for structural biologists for studying large molecular machines and membrane protein complexes at high resolutions.
Three of the world leaders in cryoEM - Richard Henderson (MRC, Cambridge), Werner Kühlbrandt (MPIBP, Frankfurt) and Sriram Subramaniam (NIH, Bethesda) - are joining the editorial board of IUCrJ to serve the cryoEM community and provide leadership for the enthusiastic acceptance of the journal by this expanding field.
On the occasion of the launch of cryoEM in IUCrJ, Richard Henderson said “There has been a quantum leap in the power of single particle cryoEM due to recent improvements in microscopes, detectors and computer programs. It is entirely appropriate that the IUCr should become the home for cryoEM in the same way as it has nurtured X-ray and other crystallographies since its foundation in 1948.”
The organizing Committee of SAS2015 is pleased to announce that the 2015 Guinier Prize winner is Professor Sow-Hsin Chen from the Department of Nuclear Science and Engineering of the Massachusetts Institute of Technology (MIT), USA. The Guinier Prize, sponsored by the International Union of Crystallography (IUCr), recognizes lifetime achievement, a major breakthrough or an outstanding contribution to the field of small-angle scattering. Over his 50-year career, Professor Sow-Hsin Chen has made numerous original and novel contributions employing small-angle scattering in fundamental studies of soft condensed matter physics. He is one of the premier scientists and experts in the international scattering community. Hallmarks of his distinguished career include the development of new methods for data analysis, together with pioneering experiments on the structure and mutual interactions of self-assembled systems such as micelles, microemulsions and protein-surfactant complexes in solution. He has trained a significant portion of the next generation of researchers in the field, including 45 PhD students. In addition, he has written a comprehensive text book on scattering methods in complex fluids. Professor Chen will receive his prize and present a plenary lecture at the SAS2015, the 16th International conference on Small-Angle Scattering in Berlin, 13-18 September, 2015 (https://www.helmholtz-berlin.de/events/sas/).
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100,000 mark, with more than 90,000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution has passed 600 and this is likely to continue to grow rapidly with Diffraction Limited Synchrotron Radiation sources (DLSR) such as MAX IV (Sweden) and SIRIUS (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites.
Neutron macromolecular crystallography is also gaining ground. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems are being successfully studied.
Neutron crystallography remains in pole position for diffraction data to be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons.
In a recent paper a group of scientists from France and the UK [Blakeley et al. (2015). IUCrJ. 2, 464-474; http://dx.doi.org/10.1107/S2052252515011239] outline the current rise in status of sub-atomic X-ray and neutron macromolecular crystallography and outline future prospects for combined approaches.
These trends are set to continue through further improvements planned to existing instrumentation, such as the addition of new detectors and the construction of entirely new instruments, such as the TOF Laue diffractometer “NMX” at the European Spallation Source (ESS). The researchers comment, however, that despite all the advances in the field, relative to X-rays, significantly larger crystals will always be required for neutron diffraction studies, particularly with the drive towards the study of ever-larger macromolecules and complexes. It is in this sense that further development of instrumentation and methods for large crystal growth are required. Creation of laboratories dedicated to the optimization of crystal volume and quality would help increase the effectiveness of neutron macromolecular crystallography. Significant efforts are required by the neutron community and facility providers to make neutron crystallography more accessible to the wider structural biology community.
Bill Stirling, Director of ILL said “While synchrotron X-ray methods dominate the field of macromolecular structure determination, neutron diffraction remains an extremely valuable complementary technique. As this article demonstrates, the power of the neutron technique resides in the ability to determine hydrogen positions, without radiation damage issues, allowing room temperature structure determinations. Further, new advances in instrumentation, exemplified by the LADI-III diffractometer at the ILL, exploit efficient Laue techniques that allow the use of much smaller crystals than previously possible and provide rapid and accurate structural information.
I have watched the development of neutron methods in biology over more than 40 years now – it is clear to me that Matthew Blakeley and his colleagues are providing biologists with extremely valuable, indeed essential, tools that will lead to major advances in our understanding of increasingly complex macromolecules."
High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In 2009, Fabrice Gorrec from the MRC Laboratory of Molecular Biology in Cambridge (LMB) published developments about MORPHEUS, a 96-condition screen in which each condition integrates a mix of additives selected for their high occurrence in the Protein Data Bank, traditional cryoprotectant and buffer system. Recently, another paper presents the development related to MORPHEUS II, a follow-up to the original screen [Gorrec (2015). Acta Cryst. F71, 831-837; doi: 10.1107/S2053230X1500967X]. In this paper it is demonstrated that additives selected from the PDB that are under-represented in traditional screens can be combined to formulate suitable and useful conditions, not only for crystallization but the overall structure determination process.
Notably, the new screen includes protein stabilizers (e.g. sugars), heavy atoms to enable experimental phasing and glycerol-like polyols to alter the parameters of crystal cryoprotection. The suitability of the resulting novel conditions is shown by the crystallization of various protein samples produced at the Laboratory of Molecular Biology (LMB) and their efficiency is compared with commercially available conditions.
A meeting of the Working Group at the 2014 IUCr Congress in Montreal concluded that there were promising movements towards widespread deposition of raw (otherwise known as 'primary') data, but there are still a number of limiting factors. (1) With no obvious single institution to archive all crystallographic raw data, the initial strategy should be the encouragement of voluntary deposition in locations most convenient for authors (e.g. synchrotron and other instrument facilities, university and institutional repositories, domain repositories such as the Australian Synchrotron.Store). (2) Search and discovery functions across diverse locations depend on common metadata identifying and describing data sets. The obvious candidate for an identifier is the Digital Object Identifier (DOI), because of existing machinery to register and share DOI information. (3) Because molecular/atomic structural studies increasingly rely on a range of technologies and techniques, it is desirable to harmonise metadata descriptions across as many such technologies as possible. Studying the 'arrangement of atoms' in its most general sense - as well as diffraction, spectroscopy and microscopy - has long been recognized as fitting within the remit of the IUCr.
While 'metadata' enters the discussion in the context of building distributed systems for search/discover, identification and retrieval of data sets, it rapidly becomes apparent that there is much more to metadata than that. 'Metadata' is variously defined, but the general sense is that it is the information that is needed to make sense of data, to allow its reuse, validation and critical analysis. Yet such 'information' is itself data - data that collectively open doors to further avenues of study, and even new scientific insight. Standard uncertainties on atomic positions modify the weights that should be given to structural models collected in databases, and so subtly affect our understanding of chemical bonding or biological function (e.g. in knowledge-based research using the Cambridge Structural Database or Protein Data Bank). The raw intensities ignored in models based solely on Bragg peaks (i.e. diffuse scattering) can now be reanalysed to provide insights into correlated disorder. Comparison of structural models derived from X-ray crystallography or from NMR can deepen understanding of protein structure and dynamics. Analysis of diffraction intensities from different experiments can yield examples of systematic bias (or, in extreme examples, dishonest practice).
Overall, the richer the metadata available to the scientist, the greater the potential for new discoveries. Crystallography is exceptional in the richness and granularity of metadata descriptors already available, mostly in diffraction-based research, and largely owing to the data dictionaries developed within the Crystallographic Information Framework (CIF), as shown in a Satellite Symposium to ECM28. (That said, the achievements of other research communities in making available their data - such as astronomers - should also be recognized. Our enthusiastic participation in organisations such as the International Council for Science (ICSU) and its Committee on Data (CODATA) is vital, both to represent crystallography, and to learn of best practice from other research communities.)
A two-day Satellite Workshop at the forthcoming European Crystallography Meeting will survey the many uses already being made of crystallographic metadata, especially where associated with raw data capture, analysis and reuse. We will identify areas where better metadata descriptors are required, and we shall begin to look at the challenges of defining new metadata, especially in studies which do not have the clean, well-defined parameters of classical single-crystal or powder diffraction experiments. Some of the biggest challenges being faced are at the centralised synchrotron (and X-ray laser) and neutron facilities, where colossal quantities of diffraction, spectroscopy and especially microscopy raw data are being generated, and also in the databases which must organise and protect access to the fruits of all our researches in perpetuity. Attendees at ECM29 are encouraged to register and participate in this important Workshop. People unable to attend may watch the Proceedings streamed live on the Web (http://ecm29.ecanews.org/ecm29-live/). We warmly encourage the community to join us in this Workshop and in follow-up activities.John Helliwell, University of Manchester
The world’s newest and brightest synchrotron light source—the National Synchrotron Light Source II (NSLS-II) at the U.S. Department of Energy’s Brookhaven National Laboratory—has produced one of the first publications resulting from work done during the facility's science commissioning phase.
The paper [Jensen et al. (2015). IUCrJ, 2, doi: 10.1107/S2052252515012221] discusses a new way to apply a widely used local-structure analysis tool—known as atomic pair distribution function (PDF) analysis—to x-ray scattering data from thin films, quickly yielding high-quality information on the films' atomic structure. The work creates new avenues for studies of nanocrystalline thin films.
PDF provides local atomic structural information or in other words, data for neighborhoods of atoms, by yielding the distances between all pairs of atoms in the sample. These distances appear as peaks in the data. In recent years, PDF has become a standard technique in structural studies of complex materials and can be used for samples that are bulk or nanoscale, amorphous or crystalline.
The approach that Billinge and his colleagues devised leverages the high fluxes of photons coming from NSLS-II, which, together with novel data reduction methods recently developed in his group, creates data suitable for PDF analysis from a thin film. Essentially, it turns the standard grazing incidence experiment on its head: the beam is simply sent through the film from the back to the front.
The first sample studied was an amorphous iron-antimony film on an amorphous borosilicate substrate mounted perpendicular to the x-ray beam. In order to isolate the contribution from the film, the substrate contribution was first determined by measuring the scattering pattern from a clean substrate. The signal from the film is barely visible in the raw data on top of the large substrate contribution, but could be clearly extracted during data processing. This allowed for a reliable, low-noise PDF that can be modeled successfully to yield the quantitative atomic structure of the film.
The data led to high-quality PDFs for both amorphous and crystalline films—confirmed by comparison to control samples in a standard PDF setup. Based on the success of these first measurements, the Billinge group and the XPD team are now planning future experiments to watch the films crystallize in real time, in the beam.
This work shows that NSLS-II—a DOE Office of Science User Facility with ultra-bright, ultra-concentrated x-ray beams—is already proving to be a game-changer in studies of thin films, which play a vital role in a large number of technologies, including computer chips and solar cells.
This article is reprinted from material taken from Brookhaven National Laboratory, with editorial changes made by IUCr.