The IUCr Newsletter is the web magazine of the International Union of Crystallography. Since 1993, the IUCr Newsletter has been published quarterly and distributed to over 13,000 crystallographers worldwide. In August 2018, it was transformed into a dynamic digital platform with a fresh new look. Its aim remains to bring together the crystallographic community.
|
William L. Duax Patricia Potter Jane Griffin The IUCr Newsletter is distributed electronically to 13,000 crystallographers and other interested individuals in 102 countries. Articles from the Newsletter are also available on this web site by following the links on the left-hand side. Feature articles, meeting announcements and reports, information on research or other items of potential interest to crystallographers may be submitted to the editor at any time. Items will be selected for publication on the basis of suitability, content, style, timeliness and appeal. Please send contributions to: newsletter@iucr.org Matters pertaining to advertisements should also be sent to the above address. Email address changes or corrections and requests to be added to the mailing list should be accomplished through the Subscribe and Unsubscribe hyperlinks above. Reuse permissions • The original article in which the material appeared is cited. • Copyright permission is indicated by the wording "Reproduced with permission of the International Union of Crystallography Newsletter". In electronic form, this acknowledgement must be visible at the same time as the reused materials, and must be hyperlinked to the IUCr Newsletter (http://www.iucr.org/news/newsletter). Please be sure to include the following information: • The title, author(s) and page extent of the article you wish to republish, or, in the case where you do not wish to reproduce the whole article, details of the section(s) to be reproduced. • The volume/issue number and year of publication in which the article appeared, and the page numbers of the article. • Details of the publication in which you wish to reprint the Newsletter material. • If the material is being edited or amended in any way, a copy of the final material as it will appear in your publication. • Contact details for yourself, including a postal address. |
![[Cover v25n2]](https://www.iucr.org/__data/assets/image/0018/135180/cover25n2.jpg) Click here for PDF Use menu on left to access previous digital issues |
Annual Reports to the IUCr Executive Committee
The IUCr Newsletter (ISSN 1067-0696; coden IUC-NEB) is published quarterly (4x) by the International Union of Crystallography (IUCr Executive Secretary e-mail execsec@iucr.org). Members receive the IUCr Newsletter by virtue of country membership in the IUCr. Periodical postage rates paid at Buffalo, NY and additional mailing offices. POSTMASTER: Please send changes of address to IUCr Newsletter Editorial Office, c/o Hauptmann-Woodward Medical Research Institute, 700 Ellicott St. Buffalo, NY 14203 USA.
In 2019, the IUCr's publication partner, Wiley, signed a transformative agreement with Projekt DEAL, a representative of nearly 700 academic institutions in Germany. This meant that researchers at these institutions are able to publish research or review articles open access in the following IUCr Journals:
Acta Crystallographica Sections A–D and F
Journal of Applied Crystallography
Journal of Synchrotron Radiation
with no direct charge. Similar deals with Austria, Finland, Hungary, the Netherlands, Norway and Sweden followed, and we are now pleased to announce that a new agreement with Jisc means that UK-based researchers at participating institutions will also be able to publish open access in the above IUCr journals at no direct cost. The agreement aims to support and accelerate open-access publishing in the UK and is the most extensive UK-based transitional agreement, covering 138 Jisc member institutions. Researchers based at participating UK institutions can now also browse and read all Wiley and IUCr journals. Liam Earney, Executive director for digital resources at Jisc, says: “This new agreement is a step-change in the transition to open access to UK research. This agreement offers all universities within the consortium, regardless of how much or little they publish, an opportunity to rapidly transition toward full and immediate open access in a financially sustainable way.”
If, after submission, your article is accepted for publication, the IUCr will pass on details of your article to Wiley so that open access can be arranged. Open-access articles in IUCr Journals are generally more highly cited and downloaded than non-open-access articles; for more information on open access and to check that you qualify for this arrangement, see here.
Chemical history often teaches that Alfred Werner (1866–1919) was the 'Founder of Coordination Chemistry' (Kauffman, 1966). In the sense that he was responsible for the modern vision of coordination chemistry and the clear distinction between oxidation number, Hauptvalenz, and coordination number, Nebenvalenz (Constable & Housecroft, 2013; Werner, 1893, 1911, 1920), this accolade is justified. However, as Bernal & Lalancette (2020) state in their publication in Acta Crystallographica Section C: Structural Chemistry, the reality is a little more complex.
Although Werner and his co-workers in Zürich were prolific experimentalists, most of these studies were performed after the publication of his seminal work of 1893 (Werner, 1893). In writing his Beitrag zur Konstitution anorganischer Verbindungen, Werner drew extensively on the large body of experimental work published by other chemists. Bernal & Lalancette (2020) particularly identify the compounds prepared by Sophus Mads Jørgensen (Kauffman, 1959) and Otto Linné Erdmann as being key elements in the development of his coordination model. This is not the place to revamp the controversy between Werner and Jørgensen, which is adequately documented elsewhere (Kauffman, 1960; Constable, 2019), although the interpretation is currently subject to some degree of revisionism (Kragh, 1997). It is certainly true that a vast number of the compounds used by Werner in developing his model were first prepared or characterized by Jørgensen or Erdmann, but this is also not the entire story.
The coordination chemistry of cobalt started at the end of the 18th Century CE with the description of what subsequently proved to be [Co(NH3)6]3+ by Tassaert (1798). This led to an exponential expansion of interest in cobalt chemistry in the following half century or so. Although the contributions of Jørgensen or Erdmann are exceptional, the contributions of Leoppold Gmelin, Emil Dingler, Karl Georg Winkelblech (Karl Marlo), Wilhelm von Beetz, Georg Vortmann, Frederic Just Claudet, Edmond Fremy and Karl Friedrich August Rammelsberg and many others are of equal importance (Constable, 2019). Among the unsung heroes of 19th Century coordination chemistry are Friedrich August Ludwig Karl Wilhelm Genth and Oliver Wolcott Gibbs who described a vast number of cobalt compounds in a series of publications in the 1850s and 1870s (Kauffman, 1977; Genth, 1851; Gibbs, 1873, 1875a,b; Gibbs & Genth, 1857a,b,c). They were also responsible for the popularization of the names for coordination compounds based on prefixes such as luteo-, croceo- and purpureo-, based on the colour of the prototype cobalt(III) complexes.
One of Werner's arguments for the octahedral coordination of complexes such as those of cobalt(III) relied on the number of isomers that could be isolated. Compounds of the type [CoA4X2]+ (A4 = four amine N-atom donors and X = halido ligand) were a critical part of the establishment of the octahedral coordination geometry as opposed to a hexagonal planar one. Only two isomers, cis-[CoA4X2]+ and trans-[CoA4X2]+, were to be expected for octahedral complexes, whereas three would be found for a hexagonal planar one (Fig. 1). First described by Jörgensen (1889), the isolation of only two forms of [CoCl2(en)2]Cl, viz. violet cis-[CoCl2(en)2]Cl and green trans-[CoCl2(en)2]Cl, was one of the observations used to support the proposed octahedral geometry. The argument was that in no case had more than two isomers been found for [CoA4X2]+ complexes, although this is not an unambiguous establishment of the geometry, in particular because it relied on the non-observation of a third isomer.
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0008/148139/me6072fig1.png)
Figure 1. The number of isomers expected for octahedral and hexagonal planar six-coordinate complexes.
Now, 131 years after the original publication by Jörgensen, the crystal structure of a new form of [CoCl2(en)2]Cl is reported by Bernal & Lalancette (2020). This compound is a purple form that contains equal amounts of the cis-[CoCl2(en)2]Cl and trans-[CoCl2(en)2]Cl isomers. It is really quite remarkable that this purple form has not been noted before, considering that the preparation of the cis-[CoCl2(en)2]Cl and trans-[CoCl2(en)2]Cl isomers is incorporated in so many undergraduate practical courses at universities around the world. The authors speculate what might have happened if Werner had been aware of, or if his co-workers had isolated, this form. It would probably not have demolished the case for the octahedral geometry, as this was built on evidence from more compounds than [CoCl2(en)2]Cl alone. Nevertheless, it would likely have caused him some sleepless nights!
This report is both interesting and important as it allows us to reassess the early work of Werner and brings an emphasis to the occurrence of cocrystals of complexes. Although the phenomenon of cocrystallization is well-established and investigated for organic compounds and pharmaceuticals, it is less well-documented or recognized in coordination chemistry. A search in Scifinder (https://www.cas.org/products/scifinder) for the terms ‘cocrystal’ and ‘cobalt’ combined yielded 234 hits, suggesting that there is a rich area for data-mining here.
Bernal, I. & Lalancette, R. A. (2020). Acta Cryst. C76, 298–301.
Constable, E. C. (2019). Chemistry, 1, 126–163.
Constable, E. C. & Housecroft, C. E. (2013). Chem. Soc. Rev. 42, 1429–1439.
Genth, F. A. (1851). Keller-Tiedem’s Nordamerikanischer Monatsbericht für Natur- und Heilkunde, 2, 8–12.
Gibbs, W. (1873). Am. J. Sci., Ser. 3, Vol. 6, pp. 116–125.
Gibbs, W. (1875a). Proc. Am. Acad. Arts Sci. 10, 1–38.
Gibbs, W. (1875b). Proc. Am. Acad. Arts Sci. 11, 1–51.
Gibbs, W. & Genth, F. A. (1857a). Am. J. Sci. 23, 234–265.
Gibbs, W. & Genth, F. A. (1857b). Am. J. Sci. 23, 319–341.
Gibbs, W. & Genth, F. A. (1857c). Am. J. Sci. 24, 86–107.
Jörgensen, S. M. (1889). J. Prakt. Chem. 39, 1–26.
Kauffman, G. B. (1959). J. Chem. Educ. 36, 521–527.
Kauffman, G. B. (1960). Chymia, 6, 180–204.
Kauffman, G. B. (1966). In Father of Coordination Chemistry. Berlin, Heidelberg: Springer-Verlag.
Kauffman, G. B. (1977). Isis, 68, 392–403.
Kragh, H. (1997). Br. J. Hist. Sci. 30, 203–219.
Tassaert, B. M. (1798). Ann. Chim. Phys. 28, 92–107.
Werner, A. (1893). Z. Anorg. Chem. 3, 267–330.
Werner, A. (1911). In New Ideas on Inorganic Chemistry. Translated, with the author’s sanction, from the second German edition. New York, Bombay, Calcutta: Longmans, Green and Co.
Werner, A. (1920). In Neuere Anschauungen auf dem Gebiete der anorganischen Chemie, 4th ed. Braunschweig: Friedrich Vieweg & Sohn.
This article was originally published in Acta Cryst. (2020). C76, 312–313.
Acta Crystallographica E: Crystallographic Communications has recently welcomed two new Section Editors: Sean Parkin (University of Kentucky, Lexington, KY, USA; s.parkin@uky.edu) and Graciela Díaz de Delgado (Universidad de Los Andes, Mérida, Venezuela; gdiazdedelgado@gmail.com). They have joined existing Section Editors Chiara Massera and Luc Van Meervelt in further developing Acta Cryst. E in its transformation to the IUCr's open-access structural communications journal for the rapid high-quality publication of fully validated structures.
Professor Parkin, already an experienced Co-editor of both Acta Cryst. E and IUCrData, was appointed in summer 2019 to succeed former Section Editor Elena Boldyreva, who had been selected as the IUCr Journals Commissioning Editor for Chemical sciences. Sean has published widely in the chemical and crystallographic literature, including nearly 150 papers in IUCr journals (Acta Cryst. A, Acta Cryst. B, Acta Cryst. C, Acta Cryst. D, Acta Cryst. E and J. Appl. Cryst.), and has contributed to International Tables for Crystallography (Volume F). Starting with his graduate studies, Sean's career has been devoted to various aspects of structural chemistry and chemical crystallography, including their application in biology and biotechnology. He is an expert in the design, procurement and state-of-the-art application of X-ray diffractometers and crystallographic facilities, and is an experienced teacher of chemical crystallography and crystallographic methods. He is keen to bring new Co-editors on board who will increase the subject, geographical and gender diversity of the Editorial Board, and make it more reflective of Acta Cryst. E’s developing authorship and readership.
The retirement at the end of 2019 of long-standing Section Editor Helen Stoeckli-Evans, to whom we extend our sincere thanks, prompted Professor Díaz de Delgado's appointment. Graciela is already well known to the IUCr as an author (in Acta Cryst. A, Acta Cryst. C and Acta Cryst. E), reviewer, member of the IUCr Executive Committee and Chair of the IUCr Calendar Committee. Her career has been devoted to a wide range of interests in structural chemistry and chemical crystallography, and in the use of single-crystal and powder diffraction for the characterisation of materials. Of particular note are her interests in active pharmaceutical compounds and their application, as well as in natural products isolated from medicinal plants of the Venezuelan Andes. She is determined to encourage submissions from Latin America and the southern hemisphere in general, and to help potential authors, especially graduate students and postdocs, overcome the obstacles (such as structure validation issues) that may prevent them from submitting an interesting manuscript to Acta Cryst. E.
Periodontitis, commonly known as gum disease, is a chronic inflammatory disease characterized by dysregulation of the oral microbiota in the subgingival space below the gum line (Hajishengallis, 2015). Healthy gums are compromised by a proliferation of pathogenic anaerobic bacteria, most commonly the triad of Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia. These pathogens release 'virulence factors', molecules that aid their colonization and survival in the subgingival niche and their evasion of the host immune response. Synergistic interactions of the pathogenic microbes with normal oral microbiota lead to a sustained host inflammatory response, degrading periodontal tissues, eroding bone, and ultimately leading to tooth loss. Severe periodontitis affects around 10% of the human population, and health implications are not limited to oral health; the chronic inflammatory conditions precipitated by the disease can extend to systemic manifestations, contributing to risk of cardiovascular and respiratory diseases, diabetes, rheumatoid arthritis, and cancer (Hajishengallis, 2015; Peters et al., 2017).
Proteases are amongst the most abundant virulence factors produced by periodontal pathogens. These enzymes degrade host proteins to feed bacterial growth, and also serve as key mediators of immune-subversive mechanisms, for example by degrading or inactivating endogenous antimicrobial peptides and components of the host complement system (Hajishengallis, 2015). One of the proteases implicated in these activities is mirolysin, a metalloprotease secreted by T. forsythia. Mirolysin cleaves multiple components of the complement pathway to protect the pathogen against complement-mediated killing, and degrades the antimicrobial peptide LL-37, a human host defense peptide secreted by epithelial and immune cells at sites of infection (Jusko et al., 2015; Koneru et al., 2017). As a recently discovered mediator of T. forsythia survival and immune evasion, mirolysin offers a potential therapeutic target, yet until now the structural basis for its latency, activation and substrate specificity has not been defined.
In this issue of IUCrJ, Guevara, Rodriguez-Banqueri et al. report high-resolution crystal structures of promirolysin, defining the mechanism of latency of the precursor protein (Guevara et al., 2020). Like nearly all proteases, mirolysin is first produced as a zymogen, maintained in an inactive state by the presence of an N-terminal extension known as a pro-peptide, pro-segment or pro-domain (Fig. 1). Upon proteolytic cleavage of the pro-segment, the active site of a protease becomes exposed and accessible to substrates. While unified by this common theme, different clans and families of metalloproteases show myriad variations in the details of how latency is maintained and activation subsequently achieved. These variations have been carefully cataloged in over 60 crystal structures of metalloprotease zymogens, including many from the Gomis-Rüth research group (Arolas et al., 2018). Here, the group finds that the mechanism of latency of promirolysin closely resembles the cysteine switch mechanism of matrix metalloproteinases (MMPs) and a number of other zinc metallopeptidases (Morgunova et al., 1999; Arolas et al., 2018). A stretch of the pro-segment occupies the enzyme active site cleft in an orientation opposite to that of a productively bound substrate, positioning a conserved cysteine residue to bind the catalytic zinc. The cysteine side chain displaces the normally bound water molecule that plays the essential hydrolytic role in proteolysis, thus rendering the zymogen inactive.
While this basic cysteine switch mechanism of latency is well precedented, the promirolysin structure reveals a surprisingly extensive interface between the pro-segment and the catalytic domain. The zymogen structure reveals a buried surface area of 2302 Å2 between these structural elements, greater than the average buried surface area for protein–protein complexes, which is remarkable given the small size of the 34-residue pro-segment. The pro-segment and catalytic domain interact through a balance of favorable hydrophobic interactions complemented by an array of hydrogen bonds and salt bridges, the same forces that shape affinity and selectivity of intermolecular protein–protein interactions (Xu et al., 1997). The extensive nature of the broad interface between pro-segment and catalytic domain suggests the possibility that the pro-segment may be capable of inhibiting the enzyme in trans, and serving as a template for engineering protein-based mirolysin inhibitors of therapeutic utility. Similar approaches have shown promise for engineering therapeutic inhibitors of ADAM family metallopeptidases, based upon their much larger pro-domains (Moss et al., 2007; Wong et al., 2016).
Guevara, Rodriguez-Banqueri et al. further report a high-resolution structure of active mirolysin bound to a peptide product, providing insight into determinants of substrate specificity of the protease (Guevara et al., 2020). A preference of mirolysin for cleavage on the N-terminal side of basic residues (Koneru et al., 2017) is explained by the presence of an aspartate residue positioned to form a salt bridge with the substrate. This aspartate residue is conserved among the pappalysin family of metalloproteases to which mirolysin belongs, suggesting that similar specificity may be typical of the entire family, and that the mirolysin structure can offer a model to understand substrate recognition for the larger family. Additionally, this serendipitously trapped product complex may provide yet another starting point from which active site-targeted mirolysin inhibitors might be developed. A similar serendipitous discovery of a product fragment captured in a crystal structure of MMP-13 recently led to the design of a potent peptidomimetic inhibitor of this metalloprotease (Gall et al., 2019). Together the new structures of mirolysin reported here offer a window from which to understand the function of this protease in gum disease, with a glimpse of how one might inhibit this intriguing target.
Arolas, J. L., Goulas, T., Cuppari, A. & Gomis-Rüth, F. X. (2018). Chem. Rev. 118, 5581–5597.
Gall, F. M., Hohl, D., Frasson, D., Wermelinger, T., Mittl, P. R. E., Sievers, M. & Riedl, R. (2019). Angew. Chem. Int. Ed. 58, 4051–4055.
Hajishengallis, G. (2015). Nat. Rev. Immunol. 15, 30–44.
Jusko, M., Potempa, J., Mizgalska, D., Bielecka, E., Ksiazek, M., Riesbeck, K., Garred, P., Eick, S. & Blom, A. M. (2015). J. Immunol. 195, 2231–2240.
Koneru, L., Ksiazek, M., Waligorska, I., Straczek, A., Lukasik, M., Madej, M., Thøgersen, I. B., Enghild, J. J. & Potempa, J. (2017). Biol. Chem. 398, 395–409.
Morgunova, E., Tuuttila, A., Bergmann, U., Isupov, M., Lindqvist, Y., Schneider, G. & Tryggvason, K. (1999). Science 284, 1667–1670.
Moss, M. L., Bomar, M., Liu, Q., Sage, H., Dempsey, P., Lenhart, P. M., Gillispie, P. A., Stoeck, A., Wildeboer, D., Bartsch, J. W., Palmisano, R. & Zhou, P. (2007). J. Biol. Chem. 282, 35712–35721.
Peters, B. A., Wu, J., Pei, Z., Yang, L., Purdue, M. P., Freedman, N. D., Jacobs, E. J., Gapstur, S. M., Hayes, R. B. & Ahn, J. (2017). Cancer Res. 77, 6777–6787.
Wong, E., Cohen, T., Romi, E., Levin, M., Peleg, Y., Arad, U., Yaron, A., Milla, M. E. & Sagi, I. (2016). Sci. Rep. 6, 35598.
Xu, D., Tsai, C. J. & Nussinov, R. (1997). Protein Eng. 10, 999–1012.
This article was originally published in IUCrJ (2020). 7, 3–4.
The German Crystallographic Society (DGK) and the Polish Crystallographic Association (PCA) both have long-standing traditions of organizing annual events. However, this year a Joint Polish-German Crystallographic Meeting took place for the first time, gathering over 320 participants in Wrocław, Poland, from 24 to 27 February 2020. The conference chairs, Marek Główka (Lodz, Poland), Marek Wołcyrz (Wrocław, Poland), Susan Schorr (Berlin, Germany) and Udo Heinemann (Berlin, Germany), filled a four-day program with great talks and posters. Multiple scientific sessions were interspersed with plenary talks, which – judging by the attendance – were found interesting by crystallographers from very different disciplines.
![[PCA-DGK welcome]](https://www.iucr.org/__data/assets/image/0016/148102/PCA-DGK-welcome.png)
Conference chairs and organizing committee members during the welcome session of the Joint Polish-German Crystallographic Meeting 2020.
A measure of an extraordinary plenary talk is whether it can capture the undivided attention of an audience with varying backgrounds and interests. And this is exactly what happened when Rolf Hilgenfeld (Lübeck, Germany) presented his lecture on SARS and MERS viruses with a special focus on the recently emerged SARS-CoV-2 (formerly known as 2019-nCoV). The audience’s interest was initially driven by the timeliness of the topic. However, the story of solving the crystal structures of the SARS-CoV-2 main protease and its potential inhibitors, already tested on cell lines, within just days of the publication of the virus genome was captivating in itself. [The Lübeck team's research has now been published in Science.]
Traditionally, the first day of the meeting was an opportunity for the DGK award winners to be announced. Dieter Fenske (Karlsruhe, Germany) received the Carl Herrmann Medal to acknowledge his life-time achievements, especially for his research in inorganic chemistry and crystallography. The Will Kleber commemorative coin for outstanding scientific contributions went to Robert Dinnebier (Stuttgart, Germany) in recognition of his exceptional achievements in the field of powder diffraction, as well as in the training of young scientists and in the service to the research community.
This year, the Max von Laue Prize for outstanding achievements by young scientists was awarded twice for the third time in its history. Tobias Beck (Hamburg, Germany) was recognized for his work on the development and characterization of novel crystalline bio-hybrid materials, which are composed of combinations of protein container building blocks and inorganic nanoparticles. In addition, Matthias Zschornak (Dresden, Germany) was recognized for his methodical development of resonant X-ray scattering to make orbitals visible and his work on defect migration and separation in oxides under the influence of external fields. Finally, the Waltrude and Friedrich Liebau Prize promoting interdisciplinarity of crystallography was awarded to Julian Voss-Andreae (Portland, OR, USA) for his significant artistic and creative work.
The organizers provided an opportunity for 19 young crystallographers to present their work in the form of lightning talks. The jury decided to award three of them with Best Presentation Awards: Elżbieta Wątor (Kraków, Poland), Bipasha Debnatyh (Dresden, Germany) and Zhenyu Wang (Berlin, Germany).
![[PCA-DGK awards]](https://www.iucr.org/__data/assets/image/0017/148103/PCA-DGK-awards.png)
The laureates of the Best Presentation Awards, Zhenyu Wang, Bipasha Debnatyh and Elżbieta Wątor, with the jury members.
After two sessions with 128 poster presentations, three scientists were honored with Poster Awards: Götz Schuck (Berlin, Germany), Katarzyna Kurpiewska (Kraków, Poland) and Yoshimichi Hagiwara (Kyoto, Japan).
The city of Wrocław, which is a traditional location for Polish crystallography meetings, was a beautiful venue for scientific discussions that lasted long into the night. The conference dinner, organized at the amazing Afrykarium of Wrocław’s zoo, was a perfect ending to the third day of exciting talks and scientific discussions.
![[PCS-DGK sightseeing]](https://www.iucr.org/__data/assets/image/0018/148104/PCA-DGK-sightseeing.png)
Polish and German participants sightseeing after the poster session.
The joint conference – an initiative bringing together crystallographers from two neighboring countries – created a very welcome platform for promoting current research and starting new collaborations.
The XV Annual Meeting of the Argentinean Association of Crystallography (AACr) was held from 12 to 15 November 2019 in the Centro Atómico Bariloche, San Carlos de Bariloche, Río Negro, Argentina. More than 160 crystallographers from different regions of Argentina and from several other Latin American countries participated in the event. Following the Meeting, the XI School of the AACr was held at the same location from 18 to 22 November. The School addressed two topics in parallel:
Course 1: “Structural and magnetic Rietveld refinement of X-ray and neutron diffraction data”, where 35 students had the opportunity to attend lectures by Juan Rodriguez Carvajal (ILL, Grenoble, France), financed by the Maldacena Program (from Instituto Balseiro, Bariloche, Argentina), and Oscar Fabello (ILL), financed by the IUCr Visiting Professorship scheme (replacing María Teresa Fernández Diaz). In addition, many local organizers (Federico Napolitano, Liliana Mogni, Gabirela Aurelio, Martin Saleta, Dina Tobia and Adriana Serquis) participated in the tutorials and special seminars.
Course 2: “Texture and strain in polycrystalline materials”, which was run by Raúl Bolmaro (IFIR Rosario, Argentina), Javier Santisteban (Argentinian Neutron Beams Laboratory) and Florencia Malamud (Centro Atómico Bariloche).
![[Course 2]](https://www.iucr.org/__data/assets/image/0004/148144/course.png)
Students attending a Course 2 lecture.
The Local Organizing Committee obtained financial support from the IUCr, Analytical–Bruker, INBOX–Panalytical, Thermo Fisher and the local funding agency, Ministerio de Ciencia y Tecnología. The event brought together 58 participants (postdocs and PhD, MSc and undergraduate students) of different nationalities: Argentina (46), Colombia (5), Cuba (3), Venezuela (2) and Uruguay (2).
The School program consisted of a 40-hour schedule (20 hours of lectures, 18 hours for experimental and practical tutorial sessions and 2 hours for a final exam). A second practical exam was given to the students, to be completed at home and returned two weeks after the School had finished. This two-step exam was taken by 38 participants who will receive academic credit for their participation in the School.
The students were provided with an anonymous survey to obtain their opinions on different aspects of the School. The large majority of comments were positive, many of them including helpful remarks that will be of valuable help in the organization of future Schools.
In a research climate that encourages the application of ‘FAIR’ data principles (that scientific data be Findable, Accessible, Interoperable and Reusable), crystallography has been able to hold its head high. Development of the Crystallographic Information Framework has led to the standardisation of datafile formats (and, more importantly, the precise codification of machine-readable terms for describing all useful attributes of data and associated metadata). Journals have required deposition of derived data in the form of atomic positional coordinates and displacement parameters, and, in many cases, the structure factors or Rietveld profiles from which models have been derived. The value of collecting these results as aggregated collections of searchable structural models in databases and journals has been well demonstrated over the last half-century.
However, in recent years, in line with concerns about research reproducibility (a 2018 Special Collection of Nature articles illustrates concerns in a variety of disciplines), focus in crystallography has shifted towards the desirability – or need – to retain and make available the primary experimental data (‘raw’ data) coming from the instruments. The IUCr commissioned a Diffraction Data Deposition Working Group (DDDWG) to consider the motivation and value of routinely storing and making available raw data sets.
The DDDWG’s final report (2017) spanned all the IUCr Commissions and the opportunities for these communities to harness the massive increases in archiving capabilities, even for raw data. The first of 14 Recommendations was:
Authors should provide a permanent and prominent link from their article to the raw data sets which underpin their journal publication and associated database deposition of processed diffraction data (e.g. structure factor amplitudes and intensities) and coordinates, and which should obey the 'FAIR' principles.
Several case studies across biological and chemical crystallography and powder diffraction were published to demonstrate the value of preserving raw data (Helliwell et al., 2017).
At the inaugural meeting of the IUCr Committee on Data (CommDat) during the August 2017 IUCr Congress in Hyderabad, India, a start was made on discussing the Commissions’ reactions to the DDDWG's final report. Subsequent detailed discussion in the Commission on Biological Macromolecules led to an article published in IUCr Journals with a specific implementation plan encouraging the systematic archival of experimental data with trusted repositories, such as the PDB, and linking to raw data from publications where possible (such linking is available from IUCr Journals, for example) (Helliwell et al., 2019). The powder diffraction community has also begun to react to the DDDWG's final report, see for example, Aranda (2018).
However, for structural chemistry, a general hypothesis was aired during the CommDat meeting that it is not necessary for small-molecule crystallographers to make all raw data available, although there are many clear cases where this is desirable. In most cases, small-molecule data are clean and simple. If, in an ideal situation, it is possible to demonstrate that all Bragg diffraction has been accounted for, that there is nothing of interest remaining in the images and that they have been processed into structure factors appropriately, then why would it be necessary to retain the raw data?
Here follows a summary of our exploration of this hypothesis, the first step of which was a survey (announced in the IUCr Newsletter and sent to a number of individuals) questioning current raw data management practices, as these underpin the ability to make the data available in the first place. Following our summary of the survey results presented here, we will hold a chemical crystallographers’ workshop at the 2020 IUCr Congress and General Assembly from which we intend to develop initial guidance on best practices for archiving small-molecule crystallographic raw data and making it publicly available.
While our personal experiences led us to believe that the small-molecule community lagged behind other disciplines in their readiness to store and share raw data, we were curious to know if this was truly the case and, more importantly, why. The methodology used was the design of a short online survey in consultation with CommDat colleagues, which was then disseminated through various crystallographic and social networks. A total of 193 responses were received from around the world, representing a good cross-section of academia, industry, government laboratories, researchers, professors and staff crystallographers. The questions, responses and raw survey data have been deposited in the Chemical Crystallography Community grouping of the Zenodo repository here.
While a majority of survey respondents, nearly 80%, claim they do archive their raw data in response to a binary yes/no question, more probing questions reveal that our initial suspicions were largely correct. Few people archive their raw diffraction data in a systematic, searchable, robust and secure way. In the main, data archiving is predominately performed 'in-house' – that is, on laboratory or office computers and with little backup, either off-site or to a secondary hard drive. Only a very few respondents store their raw data on facility/institutional archives, and almost nobody uses an independent or commercial cloud-based approach.
![[Fig1piechart]](https://www.iucr.org/__data/assets/image/0007/147886/Fig1piechart.jpg)
For those who do archive their raw data, more than a quarter have no management of their archives. The rest claim some management practices, though these are often 'dark', i.e. not accessible by others and to be used only for disaster recovery, or they are intermittent and incomplete (Fig. 1). The majority of archives are not only inaccessible to all but the facility manager but also unsearchable. By unsearchable, we mean that there is no structuring of the information or indexing based on a number of key identifiers/fields. Any search capability that does exist relies on operating-system-based tools and pivots on a single identifier, such as folder name (which invariably relates to a sample identifier). Sometimes, there is additional grouping, but this is in arbitrary categories such as year of data collection or which diffractometer was used (although such categorisation may suggest suitable metadata for structuring an efficient distributed search/indexing system). This behaviour leads to a situation where only those 'in the know' are able to find data for a particular experiment. Though it is admirable that the majority of respondents to the survey do currently take some steps to back up their raw data, clearly more can be done and there are likely to be a number of 'quick wins' that can be achieved at little or no cost (a considerable contributing factor) simply by raising awareness.
The predominant culture in small-molecule crystallography appears to be somewhat protective: 152 out of 186 respondents declare that data are not made readily available to collaborators. This is likely to reflect the fact that many of these facilities are relatively small-scale enterprises run by, at most, a handful of people, many of whom have to charge service fees in order to continue operating. This is generally in sharp contrast to macromolecular crystallography facilities. Macromolecular crystallography has taken the lead in making experimental data freely available, but while many great initiatives from this community have been followed by other crystallography subdisciplines in the past, this may be an approach that is less attractive in small-molecule crystallography. Another aspect of raw data availability is compliance with mandates imposed by funding institutions to make all experimental data openly available. Of our survey respondents, more than half claimed to be unaware of funding mandates, yet suspected that they must exist. Most respondents would also be willing to follow policies to make raw data sets for funded research accessible at some time after measurement, roughly evenly split between those who would do so for all their raw data sets and those who would do so only where mandatory. There were 17 respondents who claimed that they would not comply with such a policy, even if such compliance were mandatory. Generally, the aspirations of funders in adopting these approaches are well founded, in that they want data (generally funded by taxpayers) to be more widely exploited. However, the state of policies varies significantly around the world, particularly in terms of implementation and policing. These mandates can, therefore, be very polarising in the research community and often grudgingly followed at minimum compliance levels only – they are rarely embraced for their aspirations or intentions.
To understand why some may be resistant to or unable to comply with data archiving, it is revealing to look at the reasons why facilities might not currently archive or make their data available. Forty percent of those who do not archive their raw data (14 out of 35) believe this is an unnecessary measure. However, the most common reason people don’t back up their data appears to be a lack of appropriate infrastructure. Some respondents declare a lack of ability as a reason, and we suspect, therefore, that 'infrastructure' refers not only to supplying space for storage but also to the tools required to manipulate, transform, annotate, search and validate raw data. A lack of finances is also a clearly stated factor, with more than half of respondents stating that they are unwilling to absorb the costs associated with archiving and managing raw data. The current funding and operating models of small-molecule crystallography facilities are quite simply unable to cater to these aspects – this is unlikely to change and points to the requirement for community-level and centralised solutions and approaches.
A key factor often overlooked in data management activities is incentivisation. Initially, there is often resistance to changes in routine practice, and when these changes are imposed by external institutions or funding agencies, they are all too often viewed as punitive. It is, therefore, important to understand what our community sees as the value of good data management and to articulate this clearly. Responses to the survey in this regard were generally positive, with many of the opinion that making raw data available would enable new scientific insights (Fig. 2). Validation of results is a clear driver for making data available, while training and methods development were also considered worthy incentives.
![[Fig2chart]](https://www.iucr.org/__data/assets/image/0006/147903/Fig2chart.jpg)
It is also worth noting that this discussion has centred around service crystallography – the predominant mode of operation for most facilities. However, there is a large and growing element of crystallography that we will group here as 'advanced techniques', including, but by no means limited to, quantum crystallography, dynamic crystallography (covering numerous methods), neutron scattering, electron diffraction, nuclear magnetic resonance crystallography and diffuse-scattering analysis. These advanced techniques are becoming foundational methods for many areas of research – and generally produce diffraction data of a lower standard (or requiring a deeper level of analysis) than that commonly accepted in service crystallography. Arguably, it is these advanced techniques that will have the strongest need for robust raw data management, validation and sharing – although there will of course be commonalities with some of the tougher service crystallography examples such as disordered and incommensurate structures. In all of these cases, the drivers for sharing will be to generate further insight – or that future methods might be able to extract more information without the need to repeat the experiment.
Centralised neutron facilities have had an established approach to raw data preservation for some time and this has more recently led to a greater degree of availability as the ability to 'publish' has developed, i.e. repository capability of assigning DOIs and opening up to the internet – see, for example, ILL and ISIS data management and DOI policies. In the macromolecular community, raw data archiving is becoming just another part of the process of publication – largely in the face of fraud and out of a sense of being able to do a better job of modeling the structure oneself. Most small-molecule crystallographers would agree that routine well-behaved structures don’t need re-refining just to measure bond distances or angles, let alone re-integrating the entire dataset. However, the respondents of this survey do seem to agree that in cases of difficult refinements, disorder, twinning and modulation, having access to the raw diffraction images would benefit the community. Additionally, more than half of all respondents felt access to raw data was essential in examining pathological samples or for validating scientific claims and quality (Fig. 3).
![[Fig3chart]](https://www.iucr.org/__data/assets/image/0007/147904/Fig3chart.jpg)
Clearly, while the community does seem to agree that raw data archiving is a worthwhile practice, most lack the funds, capability, infrastructure and motivation to do so in a structured way (particularly one that would then readily enable wider sharing). Yet, as already proven by the macromolecular community, there is a real benefit to having raw data available. When we look back over the evolution of crystallographic data sharing, more crystallographers made more of their experimental data available once a standard format for data became available – the CIF (Crystallographic Information File). Though standard formats for sharing experimental data, e.g. FCF, existed around the same time as the CIF, it did not become routine for crystallographers to share their structure factors until relatively recently when this became an automated output of the refinement and embedded in the CIF. In the same vein, we should now consider how sharing of raw data can be made an automatic part of publishing crystallographic data. What steps can we, as a community, take to ensure this valuable practice becomes part of everyday operations? Who should bear the costs involved and the responsibility for maintaining such an archive?
In conclusion, we focus on two factors in this article – data management practice and the sharing of data to support scientific assertions or findings. While we use the term archiving to refer to data management practices in general, we understand that this includes the aspect of locking data away to keep it safe, as opposed to sharing it for the greater good. With a modest amount of culture change and relatively little extra money or effort, it should be possible for small-molecule crystallography facilities to manage their raw data so that it is easy to make it more widely available. However, without clear guidance on when to make data available and without centralized tools and infrastructure to support the process, widespread data sharing will continue to be elusive in small-molecule crystallography. Where is that guidance to come from, and who will create and maintain the necessary tools and infrastructure?
Should you wish to be part of the conversation, please join us in Prague on 22 August for a community-driven workshop addressing issues of raw data management and availability – see here for the schedule.
The authors would like to acknowledge John Helliwell and Brian McMahon for their significant input during the preparation of this article.
Aranda, M. A. G. (2018). J. Appl. Cryst. 51, 1739–1744.
Helliwell, J. R., McMahon, B., Guss, M. & Kroon-Batenburg, L. M. J. (2017). IUCrJ, 4, 714–722.
We are living in strange times, what with weeks of floods here in the UK, huge fires in Australia, fears of climate change, and, as if that is not enough, now we have the spread of the so-called coronavirus (COVID-19). Talking of which, I received a letter from Marv Hackert (Immediate Past President of the IUCr) informing us of some most exciting and timely work carried out on the structure of the spike protein in COVID-19 (see Letter to the Editor) by Jason McLellan and his team at the University of Texas in Austin, USA. The spike in question refers to the circled unit in this figure, and this is the nasty bit that helps the virus to gain entry into the cell. Don’t you love viruses?
![[Coronavirus spike]](https://www.iucr.org/__data/assets/image/0003/148116/coronavirus_spike.png)
You can read up more about this important work at
https://science.sciencemag.org/content/early/2020/02/19/science.abb2507 and
Work is proceeding on the structure of this virus around the world, for example at the Diamond Light Source (UK), Argonne (USA) and the University of Lübeck/BESSY II (Germany) – see the report of the Joint Polish-German Crystallographic Meeting 2020 in this issue of the IUCr Newsletter. If you ever needed to explain the importance of crystallography, now is the time!
Also in this issue, we have an article from Bill Clegg on the Cambridge Structural Database (CSD), an essential source of structural information. Bill provides a personal discussion of how the CSD has helped in both teaching and research. As you will surely know by now, last year the CSD reached its millionth structure. At the 32nd European Crystallographic Meeting in Vienna, Austria, there was even a cake specially made for the occasion.
![[CCDC cake]](https://www.iucr.org/__data/assets/image/0004/148117/cake.png)
Once more, Massimo Nespolo gives us insight into a topic in symmetry that is often overlooked even by trained crystallographers, namely the question of orbits. We are all familiar, at least we think we are, with the concept of Wyckoff sites, but the associated orbits are also worth understanding.
I was pleased to hear recently from the Royal Society (UK) that they were finally releasing their biographical memoirs free of charge. I was able to get them to let me publish here with Helen Eaton from the Royal Society a listing of all the scientists who have had links with crystallography (52 in all) and who, at the same time, were Fellows of the Royal Society. These memoirs are fascinating thorough accounts of the lives and achievements of deceased Fellows. You will find in this list names well known to many of you already, but also several others. No doubt in due course, there will be a memoir for Michael Woolfson who passed away recently.
The question of making available raw data is of current interest internationally. Here, we crystallographers and especially the IUCr have been well ahead of the game because, through much of the last century, crystal structure publications have often included tables of structure factors. I well remember as a graduate student many hours of delight having to copy them out by hand in order to put them into our Ferranti Pegasus Mark II computer! Here, Simon Coles and Amy Serjeant describe their raw data survey with an emphasis on small-molecule crystallography.
Finally, we tend to associate the International Atomic Energy Agency (IAEA) with nuclear energy. However, it also has been involved in accelerators, including those used in synchrotron radiation. You can read a compelling account here on this aspect of the work of the IAEA and how it is providing expertise and aid to developing countries. For instance, the construction of the SESAME synchrotron in Jordan is of significance as is the programme for African countries.
One more thing. At present, many countries are in lockdown, and here in the UK people over the age of 70 (e.g. me!) are likely to be confined to our homes for months. I think the same is, or soon will be, true elsewhere. Let us hope that the news will be better soon, but we have to be prepared for the long haul and serious changes to our way of living. No-one knows how all this will turn out. In the meantime, I hope you will all remain healthy.
The IUCr Newsletter (ISSN 1067-0696; coden IUC-NEB) is published electronically by the International Union of Crystallography. Feature articles, meeting announcements and reports, information on research or other items of potential interest to crystallographers may be submitted to the Editors at any time. Items will be selected for publication on the basis of suitability, content, style, timeliness and appeal.
Copyright © - All Rights Reserved - International Union of Crystallography
