|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.|
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.
Haptic interfaces have been readily adopted because of their intuitive ease of use and convenience. Obvious examples are the screens for your mobile phone or other computing devices where keyboards have been eliminated. This technology, which has been welcomed in everyday life, can also find a home in scientific research, especially in the case of “point and click” interfaces. The haptic interface provides the immediate “front end”. An equally powerful and parallel development has been cloud computing technology, where information and processing power can be shared between multiple users. The combination of these two technologies can provide both ease of use in information analysis and a wide area of application in sharing and making use of the analysis.
Point and click interfaces are common in many forms of instrumentation. An image is displayed and a human operator interprets that image, together with any associated data, feeding back results with the motion and click of a mouse and sometimes keyboard data entry. In the field of X-ray crystallography, the initial images that need to be interpreted are typically experiments aimed at the crystallisation of biological macromolecules. Each is viewed and classified in order to guide and optimise crystallisation efforts. If success occurs in the crystallisation step, another application of imaging occurs and the images of mounted crystals are used to position them appropriately with respect to the X-ray beam for diffraction analysis. For limited studies, point and click interfaces are convenient, but as the number of images involved begin to increase, even these user-friendly interfaces can become burdensome.
At the Hauptman-Woodward Medical Research Institute, the High-Throughput Crystallisation Screening Centre provides a crystallisation screening service sampling 1536 different chemical conditions. If a potential crystal is identified, the laboratory providing the sample then conducts optimisation experiments centred around the screening results. Once optimised, the resulting crystals are used for diffraction studies.
In a recent paper, scientists from Hauptman-Woodward, Diamond Light Source and Universities in the US [Bruno et al. (2016), J. Appl. Cryst. 49, doi:10.1107/S160057671601431X study the crystallisation outcome and how it is linked to the subsequent diffraction analysis, with the aim of facilitating or potentially eliminating an initial optimisation step. Their study focuses attention on the value and importance of the user interface and process.Embracing a haptic interface to enable the visualisation, classification and notation of experimental crystallisation data with a cloud-based database of images allows multiple collaborators to share the information and to fill the missing link between screening and diffraction characterisation. Information is passed directly to the beamline so that the crystallization screening plate can be analysed in the beam efficiently. This work broadly demonstrates the power of haptic interfaces and web computing to create a shareable scientific environment in crystallography and beyond.
The first diffraction experiment on a single crystal of copper sulfate by Max von Laue in 1912 and subsequent interpretation by Lawrence Bragg gave birth to the field of crystallography.
How does one assess the impact of a discipline such as crystallography, particularly when it spans across the sciences and requires a cultural change in the way of thinking and looking at a problem?
Crystallography, whether using electrons, neutrons or X-rays, has transformed the way we look at a problem and the level at which we wish to glean the composition of a material and its internal arrangement. Whether it is something as simple as table salt or as complex as the ribosome, crystallography has provided an insight that no other approach could demonstrate.
One hundred years after the first Nobel Prize in crystallography to Laue in 1914, crystallography still features in current awards. The 2013, 2012 and 2011 Chemistry awards went to scientists who continue to demonstrate the multidisciplinary outreach of crystallography. We congratulate all these winners and indeed the 2016 Nobel Prize winners in Physiology and Medicine (Yoshinori Ohsumi, for his discoveries of mechanisms for autophagy) and Chemistry (Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa for the design and synthesis of molecular machines). We are pleased to note that Ohsumi, Stoddart and Feringa have published some 40 papers in IUCr Journals during the period 1986-2014.
To acknowledge the impact and influence crystallography still continues to play, IUCr launched in 2014, a cross discipline open-access journal IUCrJ. The journal received its first impact factor of 5.3 in 2016, this impact factor results from our authors having the trust and confidence to submit some of their best work to the journal.
Along with many existing communities already publishing in IUCrJ, we wish to encourage the cryo-EM community to make IUCrJ their natural home. The importance of cryo-EM for structural science has been obvious to the IUCr for many years and will be an important feature of the next IUCr Congress in Hyderabad, where as well as the keynote speakers of the IUCr Gjonnes Medal (Richard Henderson and Nigel Unwin), there will be an additional keynote (Sriram Subramanian) and three microsymposia each with six talks. Like the Congress, IUCrJ aims to be a leading journal for reporting important advances in cryo-EM methods as well as significant science results from the application of cryo-EM.
We encourage you all to consider IUCrJ alongside other notable journals such as PNAS, JACS, Nature Communications and Nature Materials. The journal provides readers with an opportunity to see some excellent science in the chemical, materials and biological fields while keeping up with significant advances in instrumentation, methods and approaches. We aim to continue this unique combination of structural sciences in one place while welcoming new areas like the chemistry and materials science pertaining to two-dimensional crystals such as graphene.Samar Hasnain
Small-angle scattering is a powerful technique that can yield important structural information on macromolecular systems. The X-ray and neutron scattering analogues of the technique (SAXS and SANS, respectively) have both seen increased use in structural biology in the recent past. One of the latest developments for SAXS has been the availability of in situ size exclusion chromatography (SEC), which allows SAXS data to be collected from freshly purified sample material.
Researchers at the Institut Laue-Langevin (ILL) in collaboration with colleagues from Keele University have now reported the first application of a SEC system on a SANS instrument to biological solution scattering. This development has been possible because the high neutron fluxes currently available on the ILL SANS instruments allow datasets to be acquired using small sample volumes with exposure times that are often shorter than a minute. This capability is of particular relevance in the study of unstable biological macromolecules where aggregation or denaturation issues are a major problem.
Recently published results [Jordan et al. (2016). J. Appl. Cryst. 49, doi:10.1107/S1600576716016514] demonstrate the feasibility of the SEC-SANS approach and the fact that it brings real benefits to structural studies of aggregation-prone biomolecules that could not be measured in their monomeric state using conventional experimental arrangements.
Following this proof of concept, a dedicated chromatography system integrated with the instrument hardware and control software is planned in order to deal with new “sensitive” protein structures, while achieving better statistics and improved data post processing.
Synchrotron-radiation-based imaging diagnostics has become a reliable tool for systematic examination of chemical and biological samples in various research areas. Progress in photon flux density and advanced pixel array detectors with high spatial resolution, low noise and fast read-out, as well as fast and high-precision positioning manipulators, permit much reduced measuring time compared with solutions based on laboratory sources. Using these technologies, synchrotron radiation computed tomography (SRCT) experiments can be extended to achieve data acquisition times of less than a second for a complete three-dimensional (3D) dataset. Combined with optical flow analysis, this has enabled the development of cine-tomography, a technique that allows for the characterisation of four-dimensional (4D) spatiotemporal structure evolution of technical and biological processes.
Synchrotron radiation computed laminography (SRCL) has extended the applicability of 3D synchrotron imaging to thin plate-like objects that otherwise prohibit homogeneous transmittance using conventional tomographic scans. It is especially suited to flat specimens which cannot be trimmed down and thus do not fit into the detector’s field of view.
Due to the complexity of the experimental setup, SRCT and in particular SRCL pose challenging problems for automation and software-controlled experiment. For a successful automated scan, the imaging and sample apparatus must be aligned and positioned properly, the sample be stabilised and the measurement setup controlled during the imaging process.
A team of scientists from Germany, France and Russia [Vogelgesang et al. (2016). J. Synchrotron Rad. 23, 1254-1263; doi:10.1107/S1600577516010195] address the outlined experimental challenges by developing concepts, tools and methods for smart image recording.
Successfully employed both SRCT and SRCL are used with a large variety of contrast modes such as phase contrast, fluorescence and diffraction contrast allowing many applications in materials research, microsystem technology, cultural heritage, palaeontology and biology.