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International Union of Crystallography

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.

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Radiation damage to macromolecules: kill or cure?

RD8Radiation damage induced by X-ray beams during macromolecular diffraction experiments remains an issue of concern in structural biology. While advances in our understanding of this phenomenon, driven in part by a series of workshops in this area, undoubtedly have been and are still being made, there are still questions to be answered.

Interest in radiation damage to macromolecules during structural experiments has not abated over the last few years, since there remains a need to understand both the parameters that affect radiation damage progression (the `kill’) and also the artifacts produced by it. Although there is now a growing body of literature pertaining to this topic (see for example the special issues of the Journal of Synchrotron Radiation arising from papers presented at the 2nd to 7th International Workshops on Radiation Damage to Biological Crystalline Samples, published in 2002, 2005, 2007, 2009, 2011 and 2013, respectively), clear foolproof methods for experimenters to routinely minimize damage have yet to emerge. Additionally, radiation damage is also a concern and limiting problem in other methods used in structural biology such as electron microscopy, SAXS and scanning X-ray diffraction. However, the recently available free electron lasers (FELs) have presented the possibility and promise that samples will give 'diffraction before destruction’: is this indeed the `cure’ for the challenges of radiation damage?

For the majority of macromolecular crystallographers, using a FEL is not yet a realistic expectation. For them, radiation damage to their samples is likely to become an increasingly observed phenomenon, since much smaller X-ray beams with very high flux densities are becoming available due to upgrades in both electron storage rings and the synchrotrons that feed them. These fourth-generation synchrotrons are engendering even more interest in research into radiation damage and its deleterious effects.

It is clear from a special issue devoted to radiation damage [Garman, E. F. and Weik, M. (2015). J.Synchrotron Rad. 22] that there remains much scope for further studies to inform both experimental practice and the interpretation of the resulting structures so that radiation damage can become a widely recognised and understood facet of structural biology. These experiments on macromolecular crystals will certainly involve more `kill’ and, it is to be hoped, some `cure’ too.

Posted 26 Feb 2015 

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Data to knowledge: how to get meaning from your result

[visualisation of external restraints during refinement]Like many modern areas of science, structural biology faces enormous challenges created by the vast amount of data generated every day by research groups. As such structural and functional studies require the development of sophisticated "Big Data" technologies and software to increase the knowledge derived and ensure reproducibility of the data. A group of scientists [Berman et al. (2015). IUCrJ. 2, 45-58; doi:10.1107/S2052252514023306] present summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modelling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB "super" laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

Posted 20 Feb 2015 


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Continuing the development and expansion of Acta Crystallographica Section B

[journal cover]Two special issues were published in 2014: the first of these, on Crystal Engineering and helmed by Guest Editor Andrew D. Bond appeared in the February issue; the second in August was on Non-ambient Crystallography, with Guest Editors David G. Billing and Andrzej Katrusiak. The special issues helped promote the message of the widening scope of the journal. We had a 64% increase in the number of pages published in the journal, from 633 in 2013 to 1036 in 2014. Further special issues are in progress for 2015-2016, including those on Energy Materials (Guest Editors Simon Parsons, Richard Walton and Karena Chapman), Crystal Structure Prediction (Guest Editors Graeme Day and Carl Henrik Görbitz), and others are planned.

In 2014 the journal published its first Research Perspective article Aperiodic crystals and superspace concepts by Ewald Prize winners Ted Janssen and Aloysio Janner [Janssen, T. & Janner, A. (2014). Acta Cryst. B70, 617-651; doi:10.1107/S2052520615001663]. A research perspective is an article where the main or sole author is an established leader in a particular field and such articles are expected to review the developments of that field, with a strong focus on the author's own contributions to it. The journal will normally publish one article in this category per year and plans for 2015 are currently under way. Leading scientists are welcome to write to us with suggestions and a 500 word outline.

The journal published two feature articles in 2014, Crystalline metal-organic frameworks (MOFs): synthesis and structure and function [Dey et al. (2014). Acta Cryst. B70, 3-10; doi:10.1107/S2052520613029557] and Crystallographic studies of gas sorption in metal-organic frameworks [Carrington et al. (2014). Acta Cryst. B70, 404-422; doi: 10.1107/S2052520614009834]. Future feature articles will include MOFs under high pressure by Stephen Moggach, Prospects for crystal engineering by Christer Aakeröy and contributions by several high-profile speakers at the Montreal IUCr Congress.

Commentaries on some outstanding articles are now appearing regularly in the journal, and we would like to thank the authors of these for their rapid and valuable contributions. Other articles have been highlighted by means of regular news features on the IUCr homepage. The Acta B homepage will be redesigned for 2015, to allow more extensive coverage of recent news items and to highlight outstanding articles and the most cited papers from the journal.

Acta B has an established reputation for publishing work in fields such as aperiodic structures and high-pressure crystallography, and we are working to expand our coverage, including in other areas of materials science and crystal engineering. Acta B has much to offer authors, including speed of publication and high but practical technical standards.

We note that the number of papers where the authors have opted for open access is on the rise: such papers are amongst the most downloaded for the journal.

Finally, the journal will be represented at a number of meetings in 2015, including at the 12th International Conference on Materials Chemistry (MC12, York, UK), the Annual Meeting of the American Crystallographic Association (Philadelphia), and at the 29th European Crystallographic Meeting (ECM29, Rovinj, Croatia). You can see a full list of meetings where IUCr Journals will be displayed by following this link.

This is an excerpt taken from the full editorial which can be found at:
Blake, A. & de Boissieu, M. Acta Cryst. (2015). B71, 1-2; doi:10.1107/S2052520615001663

Posted 17 Feb 2015 

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The revival of the Bravais lattice

[Auguste Bravais]The following short quiz will test your knowledge and understanding of the Bravais lattice.

(1) What are the Bravais-lattice symbols of the following space groups: No. 2, No. 40, No. 150 and No. 161?

(2) What is the essential geometric difference between the Bravais-lattice types mP and mS? Note: The correct answer contains neither the words 'affine equivalent' nor the words 'unit cell'. Try also the Bravais-lattice types oP, oS, oF and oI.

The 14 Bravais-lattice types are at the very heart of crystallography. It is somewhat remarkable that, in the second decade of the 21st Century, we may still learn new things about them. In Grimmer's paper [Grimmer, H. (2015). Acta Cryst. A71, doi:10.1107/S2053273314027351] he does just this and provides important new insights. Grimmer presents an entirely original way of determining the hierarchical arrangement of Bravais-lattice types. The result is summarised in an easily understood figure. In the figure, the Bravais-lattice type at the upper end of a line is a special case of the type at its lower end. Grimmer's approach to determining the hierarchy is to examine the group-subgroup relations amongst the space groups of the Bravais-lattice types. The latter are those (14) symmorphic space groups with the point group of a holohedry.

[Flack, H.D. (2015). Acta Cryst. A71, doi:10.1107/S2053273315002557]

Posted 24 Feb 2015

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Fluorescence-based protein crystal identification

en5560Successful protein crystallization screening experiments are dependent upon the experimenter being able to identify positive outcomes. The introduction of fluorescence techniques has brought a powerful and versatile tool to the aid of the crystal grower. Trace fluorescent labeling, in which a fluorescent probe is covalently bound to a subpopulation of the protein, enables the use of visible fluorescence. Alternatively one can avoid covalent modification and use UV fluorescence, exploiting the intrinsic fluorescent amino acids present in most proteins. By the use of these techniques, crystals that had previously been obscured in the crystallization drop can readily be identified and distinguished from amorphous precipitate or salt crystals.

Overall, fluorescence, whether intrinsic or by using trace fluorescent labeling (TFL), can be a powerful aid in macromolecule crystallization. Here Meyer et al. [(2015). Acta Cryst. F71, 121-131; doi:10.1107/S2053230X15000114] have only discussed its use in screening for crystals, although other applications in the field of macromolecule crystallization and crystal growth are possible. Simple instrumentation incorporating the requisite basic functionality for the three main approaches discussed in the paper can be realized in even a small structural biology laboratory. The benefits obtained are powerful aids in interpreting the screening results as well as obtaining potential insights leading to additional, previously unrealized, lead conditions.

Posted 11 Feb 2015 

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Dispersion-corrected density functional theory (DFT-D)

[YIRVOL: overlay of original (red) and corrected (blue) experimental structures]Powder diffraction data rarely provide all the structural detail a crystallographer needs. But, if theoretical calculations in the form of dispersion-corrected density functional theory (DFT-D) can validate the data, then for structures where sufficiently large crystals are inaccessible the picture can be made clearer.

In 2010, Jacco van de Streek and Marcus Neumann of the University of Copenhagen, Denmark and Avant-garde-Materials Simulation, in Germany, tested the concept against data sets from 225 high-quality single-crystal determinations of organic molecules as a benchmark. The team reported that DFT-D offers a good approximation for those molecules, Now, the team has verified that the approach works with powder data on 215 sample organic structures each published in an IUCr journal identified through a search of the Cambridge Structural Database [van de Streek, J. & Neumann, M. A. (2014), Acta Cryst. B70, 1020-1032; doi: 10.1107/S2052520614022902].

The team points out that density functional theory techniques of all the approaches to quantum mechanical calculations for molecules offer a favorable trade-off between accuracy and speed.

They report that three of the 2010 batch of 225 published single crystal structures were found to be incorrect. In contrast, almost 9 percent (19 of the 215 powder structures) were "demonstrably in error". The team does reassure us that the majority of those erroneous structures were only incorrect in minor ways - minor space-group revisions, exchanges of atoms with similar electron densities such as a carbon for a nitrogen, and ambiguities involving hydrogen atoms, for example where hydrogen bonding was involved. They add that some ambiguities were reported by the authors of the original papers but those authors did not have available to them the tools to remedy this situation.

van de Streek and Neumann have now demonstrated that not only can Dispersion-corrected Density Functional Theory (DFT-D) calculations provide "an independent source of structural information about organic crystal structures" to help improve the structures obtained, they can corroborate or counter claims for a given structure. Moreover, this and the 2010 study offer a warning to users of powder diffraction analysis regarding an often hard to detect phenomenon called "preferred orientation", in which the measured data are biased and do not accurately reflect the underlying crystal structure. The team found that the most troublesome ambiguities were manifest in those studies in which preferred orientation was present. This phenomenon should, the team suggests, be treated with greater suspicion than is currently the case when reporting a "definitive" crystal structure.

Talking to the IUCr, van de Streek told us "The main limitation of the DFT-D approach is that only static structures can be addressed and we are currently investigating methods to include the effects of temperature such as thermal expansion and disorder".

Posted 09 Feb 2015