COVID-19 and cryo-EM

Volume 28, Number 2, 2020

ISSN 1067-0696

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IUCr journals news

Rapid publication of SARS-CoV-2/COVID-19 research in IUCr Journals
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IUCr journals news

Two new virtual special issues of Journal of Synchrotron Radiation
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Two new virtual special issues of Journal of Synchrotron Radiation

PhotonDiag2018 Workshop special issue

The Journal of Synchrotron Radiation's first virtual special issue contains some highlights of the PhotonDiag2018 Workshop on FEL Photon Diagnostics, Instrumentation, and Beamlines Design, which took place in Hamburg, Germany, in September 2018. The workshop, the fourth in the PhotonDiag series, focused on advances in X-ray optics and photon diagnostics, one of the most dynamically evolving topics in the X-ray science world.

Guest-edited by Daniele Cocco, Jan Grünert, Elke Ploenjes, Kai Tiedtke and Marco Zangrando, these virtual proceedings start with the articles focused on diagnostics to study the spectral distribution, the wavefront, the intensity, the profile, the polarization and the temporal distribution. The combined use of photon diagnostics and electron diagnostics to study machine performance follows, and the third part deals with more conventional X-ray optics, from metrology over adaptive focusing mirrors to crystal monochromators. The proceedings close with one crucial component to most experiments and diagnostics, i.e. the X-ray detectors.

X-ray Free-Electron Lasers special issue

The last five years have seen a remarkable explosion in both the availability and capabilities of X-ray free-electron lasers (XFELs). Considering this rapid progress, it was considered timely for another special FEL-related issue in the Journal of Synchrotron Radiation, following the first one published in May 2015. The current virtual edition, guest-edited by P. H. Fuoss, I. Schlichting, T. Tschentscher and M. Yabashi, provides information to guide both X-ray experts and new users.

The issue features articles describing a variety of sources and facilities, including FLASH, LCLS, SACLA, SwissFEL, PAL and EuXFEL, that give insight into the current status, development plans and scientific directions at these facilities. Papers focused on individual instruments provide detailed information into new experimental capabilities along with recent results highlighting the scientific opportunities being developed at XFELs. Overviews of the design and performance of important subsystems, for example laser systems for time-resolved measurements, give critical information to plan successful XFEL experiments. In particular, a number of papers focus on the infrastructure requirements and challenges at the European XFEL, the first of the next generation of megahertz repetition rate XFEL producing hard (≲1 Å wavelength) X-rays. Finally, new X-ray scientific methods are constantly being ported to, and developed at, FEL sources. This edition highlights a few of these capabilities including spectroscopy techniques.

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Commentary

Making sense of vacancy correlations with single-crystal diffuse scattering data
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Making sense of vacancy correlations with single-crystal diffuse scattering data

Matthew Krogstad

Figure 1. Scattering data from simulated crystals of Nb_1-xCoSb from Roth et al. (2020). For x = 1/4, an ordered state is produced where there are no nearest-neighbor vacancies, producing a commensurate set of superstructure peaks, and for x = 1/6, next-nearest neighbors can be completely avoided as well, producing eight-point rings when appropriately twinned. For concentrations with 1/4 > x > 1/6, a disordered mixture of the two states is shown to minimize energy compared to proposed ordered states and reproduces observed scattering in this range. For concentrations with x < 1/6, disordered states produce broad rings and waves.

Local ordering of atoms within a crystalline structure is increasingly recognized as essential to understanding the properties of a variety of interesting materials. This is shown by the success of pair distribution function (PDF) analysis of scattering data from powder samples to investigate departures from perfectly crystalline order (Billinge & Kanatzidis, 2004; Egami & Billinge, 2012). Diffuse scattering from single crystals can also be a powerful probe of local order, potentially providing key information that would be difficult to obtain from PDF methods; however, difficulties in both measurement and interpretation of data have too often restricted their use by a larger community. In this issue of IUCrJ, Roth et al. (2020) demonstrate how simple concepts can be applied to better understand single-crystal diffuse scattering from half-Heusler systems.

Recent developments in instrumentation and computing have made the measurement of single-crystal diffuse scattering much easier than it was even ten years ago (Ye et al., 2018; Keen et al., 2015). Valuable data can also be obtained with lab-based X-ray sources and electron sources, which are able to produce high-quality data in a carefully chosen set of planes (Izquierdo et al., 2011; Welberry & Goossens, 2016). However, the analysis of such data can still seem a daunting task, especially when compared to the powder-based PDF data. A key step for proposed solutions is comparison of experimental scattering data with those from simulated structures, but it can be difficult to connect diffuse scattering from simulated structures to specific structural motifs.

Roth et al. (2020) have produced a compelling analysis of diffuse scattering from half-Heusler materials Nb_1-xCoSb. These have proven challenging to understand via crystallographic techniques; while crystallographic solutions can confirm the concentration of vacancies on the Nb sites, the distribution of these vacancies is more difficult to discern. Electron diffraction data collected by Xia et al. (2018, 2019) show clear diffuse scattering patterns over a range of concentrations, implying that vacancies are spatially correlated locally without being ordered over the entire structure. Simulations based on density functional theory (DFT) have reproduced the scattering for certain concentrations but cannot be generalized over the full range of vacancy concentrations and provide limited insight into the systematics of local structures in these systems.

Roth et al. (2020) approach these data starting with the simple concept that Nb site vacancies will tend to avoid one another. Simulated crystals are then generated by a Monte Carlo procedure which allows vacancies to move and penalizes vacancies being nearest-neighbors and next-nearest neighbors via a simple Ising-like model. Diffuse scattering from these models is rapidly calculated using the program SCATTY (Paddison, 2019). While the number of individual states produced by these models is quite large, the only free parameters are the vacancy concentration, the ratio between energies associated with nearest and next-nearest neighbors, and the temperature.

For a single ratio of energies, these models impressively reproduce published electron diffraction data over a range of vacancy concentrations (see Fig. 1). Distinct ordered ground states are reproduced at x = 1/4 and x = 1/6, with intermediate compositions showing short-range combinations of the two. For concentrations with x < 1/6, broader wave-like scattering is seen. This entire range of compositions can be modeled and explained with self-avoiding vacancies.

These results provide a significant advance in the knowledge of the structure of these materials as well as a great example of how short-range ordering can be understood, modeled and described. Roth et al. (2020) have provided a clear picture of occupational correlations in half-Heusler compounds. With single-crystal diffuse scattering data becoming easier to obtain, the use of simple models of short-range substitutional correlations is a key method for understanding such data.

Acknowledgements

This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

References

Billinge, S. J. L. & Kanatzidis, M. G. (2004). Chem. Commun. pp. 749–760.

Egami, T. & Billinge, S. J. L. (2012). Underneath the Bragg peaks: structural analysis of complex materials. Oxford: Elsevier.

Izquierdo, M., Megtert, S., Colson, D., Honkimäki, V., Forget, A., Raffy, H. & Comès, R. (2011). J. Phys. Chem. Solids, 72, 545–548.

Keen, D. & Goodwin, A. (2015). Nature, 521, 303–309.

Paddison, J. A. M. (2019). Acta Cryst. A75, 14–24.

Roth, N., Zhu, T. & Iversen, B. B. (2020). IUCrJ, 7, 673–680.

Welberry, T. R. & Goossens, D. J. (2016). IUCrJ, 3, 309–318.

Xia, K., Liu, Y., Anand, S., Snyder, G. J., Xin, J., Yu, J., Zhao, X. & Zhu, T. (2018). Adv. Funct. Mater. 28, 1705845.

Xia, K., Nan, P., Tan, S., Wang, Y., Ge, B., Zhang, W., Anand, S., Zhao, X., Snyder, G. J. & Zhu, T. (2019). Energy Environ. Sci. 12, 1568–1574.

Ye, F., Liu, Y., Whitfield, R., Osborn, R. & Rosenkranz, S. (2018). J. Appl. Cryst. 51, 315–322.

This article was originally published in IUCrJ (2020). 7, 579–580.

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Editorial

COVID-19 and cryo-EM
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COVID-19 and cryo-EM

Sriram Subramaniam

The last few years have seen spectacular growth in the widespread adoption of cryoelectron microscopy (cryo-EM). With the advent of direct electron detectors, the number of depositions in the EM Data Bank (EMDB) has increased steadily at a rate of ~30% every year since 2014, crossing the 10 000 mark in early 2020.

What may not be widely appreciated is that this extraordinary rate of growth in cryo-EM is not new. The number of depositions in the EM data repository increased on average by ~40% each year between 2004 and 2014, quickly expanding beyond the 52 entries listed in 2004. Besides the sheer increase in numbers of structures being determined using cryo-EM methods, an important aspect to this growth is the application of cryo-EM to determine structures of heterogeneous and dynamic assemblies. Protein complexes of this kind will most likely continue to remain largely intractable to crystallographic approaches that require the generation of ordered two- or three-dimensional crystals.

The rapid progress in the application of cryo-EM methods to study SARS-CoV-2 proteins provides a convincing demonstration of the power of cryo-EM in the arsenal of structural biology. Within a month or so of the availability of the gene sequence, Wrapp et al. (2020) and Walls et al. (2020) were able to obtain the first structures of the soluble part of the trimeric SARS-CoV-2 spike protein. Nearly a dozen groups worldwide have extended these studies in short order to decipher many conformational variants of the spike protein, including structures of native spikes displayed on intact viral membranes. These are major achievements that are also a testament to the speed, quality and biomedical relevance of present day cryo-EM methods. The structures provide important insights into the complexity of spike architecture, especially in the conformational spread of the domain that binds the human ACE2 receptor. These studies, in combination with emerging structural information on the binding sites of various antibodies on the S-protein are fundamentally relevant to the design of effective therapeutics and vaccines against COVID-19.

Before January 2020, of the 84 coronavirus cryo-EM structures deposited in the repository, 82 were of trimeric spike proteins. In contrast, of the 34 entries related to SARS-CoV-2 that have been deposited in 2020, only ~50% are of spike proteins, with the rest coming from entries such as the ORF3a membrane protein, ACE2 protein in complex with the membrane protein BOAT1 and RNA polymerase complexes in different conformational states [Fig. 1(a)]. What is noteworthy about these advances is that protein complexes of this kind are often flexible and conformationally heterogeneous, making them challenging to study by X-ray crystallography. The advent of ‘single particle’ methods such as cryo-EM and XFELs offer the exciting prospect to transcend the description of proteins in terms of static structures, and instead derive conformational landscapes that may provide a much better way to understand their biological function (Ourmazd, 2019). We are now publishing an increasing number of important papers in this area in IUCrJ, and are particularly keen to welcome papers in IUCrJ and other IUCr journals that increase understanding of SARS-CoV-2.

The realization of the potential impact of cryo-EM led to the nucleation of several national and regional facilities in different countries to nurture the growth of the cryoEM field (Subramaniam, 2019). While these facilities continue to play a key role, we are now seeing growth in the cryo-EM field that is fueled by the increased availability of high-end cryo-EM instrumentation within individual institutions. For this trend to continue, it is critical that the cost of cryo-EM instrumentation necessary for high-resolution structure determination decreases significantly. Funders of biomedical research need to encourage manufacturers to drive costs down to allow the technology to be accessed more readily by the larger biological community.

The critical role played by the EMDB over the last two decades in the dissemination and impact of cryo-EM cannot be underestimated. Established at a time far before the wider recognition of the cryo-EM revolution, the access provided by the repository of structures to both specialists and nonspecialists has catalyzed the growth of the field enormously. The recent launch of EMPIAR as an archive where authors are able to deposit raw cryo-EM data has enabled crowdsourcing of data analysis. I enthusiastically endorse their appeal to the structural biology community to deposit COVID-19-related raw cryo-EM data in EMPIAR to enable more in-depth analysis following initial publication of the data given the rapid growth in our collective knowledge of this pandemic.

While cryo-EM techniques are being used to glean atomic level information on SARS-CoV-2, it is worth reflecting on the historical context of electron microscopy in the study of these types of viruses. In the 1960s, a young technician named June Almeida made seminal observations in the course of electron microscopic investigations of viruses. Almeida, who trained initially in Canada and subsequently worked at a hospital in London, showed that antibodies derived from infected individuals could be used to coat viruses, thereby enabling their detection in the electron microscope using heavy-atom stains to generate contrast. Among her many contributions to the imaging of viruses such as Rubella and hepatitis B in an electron microscope, one that stood out was the observation of a new kind of virus that she and her colleagues labeled as a ‘coronavirus’ in recognition of the viral surface proteins, which appeared like a crown or ‘corona’ on the membrane.

Figure 1. (a) A selection of recently reported cryo-EM structures of SARS-CoV-2 proteins including spike proteins, RNA polymerase complexes and membrane proteins in the viral envelope. The PDB identifiers of the structures are indicated. (b) Negatively stained transmission electron microscopic image (Almeida & Tyrrell, 1967) of a novel virus that was named a ‘coronavirus’ by June Almeida in 1966. (c) Colorized transmission electron microscope image of negatively stained infectious SARS-CoV-2 particles recorded at NIAID’s Rocky Mountain Laboratories (RML) in Hamilton, Montana. The arrows in panels (b) and (c) point to the spike proteins on the surface of the virus particles.

The resemblance of June Almeida’s image from 1966 [Fig. 1(b)] of a sample referred to as B814 and the iconic recent image of the SARS-2 coronavirus [Fig. 1(c)] produced by scientists at the NIAID laboratories in Montana is remarkable. Looking ahead, a major goal of structural virology will be to bridge the gap between the knowledge of atomic resolution structures of individual viral components and the critical macromolecular interactions that define their assembly along with RNA into an intact, infectious virus. These kinds of integrative structural studies, combined with biological analyses of the processes involved in viral replication will be essential to understand the molecular mechanisms by which SARS-CoV-2 enters cells to cause its devastating effects on human health.

References

Almeida, J. D. & Tyrrell, D. A. J. (1967). J. Gen. Virol. 1, 175–178.

Ourmazd, A. (2019). Nat. Methods, 16, 941–944.

Subramaniam, S. (2019). IUCrJ, 6, 1–2.

Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T. & Veesler, D. (2020). Cell, 181, 281–292.e6.

Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S. & McLellan, J. S. (2020). Science, 367, 1260–1263.

Sriram Subramaniam is Gobind Khorana Chair for Cancer Drug Design and Canada Excellence Research Chair at the University of British Columbia, Vancouver BC V6T 1Z3, Canada.

This article was originally published in IUCrJ (2020). 7, 575–576.

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Commentary

Combining forces: complementary techniques brought together to determine tricky crystal structures
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Combining forces: complementary techniques brought together to determine tricky crystal structures

Graeme M. Day

In a recent issue of Acta Crystallographica Section B, Dudek et al. (2020) report the determination of two crystal structures of the pharmaceutical molecule furazidin, whose existence has been reported in patents, but whose structures have to date been uncharacterized. The work shows how multiple techniques – powder X-ray diffraction, nuclear magnetic resonance (NMR) spectroscopy and computational crystal structure prediction (CSP) – are sometimes required to determine crystal structures of organic molecules when direct determination from diffraction data is not possible, and demonstrates the complementarity of information provided by the different methods.

Crystallization of furazidin in this work produced microcrystalline powders and no single crystals that could be used for crystal structure determination. This is a common problem that can frustrate attempts to understand the structure of a material. However, developments in applying NMR techniques to solids, along with quantum mechanical methods that can provide accurate predicted NMR parameters from putative structures, can offer an alternative to diffraction-based structure solution. This approach of determining a crystal structure by constructing or identifying a structural model that reproduces the observed NMR spectra is termed NMR crystallography. A challenging stage in applying NMR crystallography is the generation of realistic structural models to which quantum mechanical predictions of NMR parameters can be applied.

This is where CSP has entered the field of NMR crystallography; computational methods for CSP have been developed to predict, from nothing more than the chemical diagram, the likely crystal packings of a molecule. While CSP is often discussed as an ab initio method, requiring no input of experimental data, these methods can also be combined with experiment, providing the missing ingredient in NMR crystallography determination of structures. The process seems simple: apply CSP to predict possible crystal structures, perform calculations to predict the NMR parameters for the best predicted structures and compare these with the measured NMR spectra. However, CSP for molecules of the size and flexibility of furazidin is challenging, particularly when the experimental information shows that there are two symmetrically unrelated molecules in one of the polymorphs. CSP is relied on in this method to locate all possible structures, which correspond to local energy minima on the energy surface defined by all degrees of freedom of the crystal structure. Molecular flexibility and multiple independent molecules add to these degrees of freedom and lead to very large numbers of energy minima, often numbering in the hundreds or thousands within the usual energetic range of polymorphism. This creates a computational challenge in itself – the location of all possible structures – and creates a second problem for NMR crystallography: within a large set of computer-generated crystal structures, one can find false-positive agreement with the measured NMR spectra. These are structures where calculated chemical shifts seem to be close enough to experiment (within the errors of the quantum mechanical methods used to predict the NMR), but where this agreement is fortuitous, and the structure is incorrect.

The complexity of CSP is reduced in this work by identifying constraints from the experimental data to the degrees of freedom that need to be explored. Diffraction data and NMR are able to provide complementary views of the structure; NMR gives local structural information, reporting on molecular geometry, close contacts and nearest neighbour interactions, while the most readily extracted information from diffraction is the long-range periodicity of the molecular arrangement. Powder X-ray diffraction was used to narrow the list of possible space-group symmetries that needed to be considered during structure prediction, while NMR provided information to narrow the set of molecular conformations, which further reduced the search space. This led to a tractable CSP problem.

The issue of false positives was addressed by comparing calculated and measured NMR parameters for multiple nuclei – here, both ¹H and ¹³C. While incorrect structures sometimes reproduced either the measured ¹H or ¹³C chemical shifts, only one structure for each polymorph was found to reproduce both. This in an important message from this study: not to rely solely on ¹H or ¹³C data because of the risk that agreement with experiment is spurious.

The report by Dudek and coworkers of integrating these techniques – diffraction, NMR and structure prediction – to determine crystal structures that could not have been determined using a single method is an important example that nicely illustrates the process and demonstrates the importance of careful validation.

References

Dudek, M. K., Paluch, P. & Pindelska, E. (2020). Acta Cryst. B76, 322–335.

This article was originally published in Acta Cryst. (2020). B76, 294–295.

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Commentary

Shock-synthesized quasicrystals
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Shock-synthesized quasicrystals

Péter Németh

Figure 1. The Al₆₂Cu₃₁Fe₇ icosahedral quasicrystal revealing fivefold rotation and its coexisting Cu–Al phase assemblage of stolperite (β, AlCu) + khatyrkite (θ, Al₂Cu) from a laboratory-shocked sample. Adapted from Hu et al. (2020).

Impact-processing of planetary materials and laboratory-shock experiments are of great interest. During these extreme processes a hypervelocity shock wave generates extremely high pressure and high temperature for exceptionally short times (micro- and nanoseconds) and provides favourable conditions for the formation of peculiar structures. In a recent IUCrJ article, Hu et al. (2020) report the shock synthesis of an unusual material, the icosahedral Al₆₂Cu₃₁Fe₇ quasicrystal (QC), which was previously identified in the Khatyrka meteorite (Bindi et al., 2016).

QCs are a unique type of material, which are characterized by sharp diffraction features and possess symmetry elements that apparently are inconsistent with the conventional rules of crystallography. In particular, the first Al₈₆Mn₁₄ alloy QC to be recognized has icosahedral symmetry featuring among other things fivefold rotation axes (Shechtman et al., 1984). The appearance of these unconventional rotations triggered exciting discussions right from the first report [reviewed in Prodan et al. (2017) and https://paulingblog.wordpress.com/tag/quasicrystals/]. On the one hand, Shechtman and colleagues presented QCs as a new type of crystalline material, in which atoms are repeated according to a quasiperiodic translation (Lifshitz, 2003). The interpretation of the QCs’ structure was also approached with the so-called Amman tiling, the 3D equivalent of the 2D Penrose tiling (Lord et al., 2000). On the other hand, Pauling insisted that no crystallographic rules were violated and considered QCs as multiply twinned cubic structures (e.g. Pauling, 1985). Although it turned out that Pauling’s interpretation did not hold, recently Prodan et al. (2017) reported that QCs could in fact be interpreted as multiply twinned structures, considering the unit cell of the primitive golden rhombohedra, and demonstrated that ‘tiling’ and ‘multiple twinning’ are fully compatible with each other. However, this interpretation requires the occurrence of equal size twin domains, which is uncommon in nature. In either way, the crystallographic identity of QCs seems to be still debated.

Since their discoveries, over a hundred QCs have been described from syntheses. In contrast, only a few studies report QCs from natural materials and, in fact, all have been associated with the Khatyrka meteorite. So far three new QC types have been described from this meteorite: the i-phase I with composition of Al₆₃Cu₂₄Fe₁₃, officially named icosa-hedrite (Bindi et al., 2009); the d-phase with composition of Al₇₁Ni₂₄Fe₅, referred to as decagonite (Bindi et al., 2015); and the i-phase II with Al₆₂Cu₃₁Fe₇ composition (Bindi et al., 2016). However, this list perhaps can be extended with additional extraterrestrial phases (personal communication with Luca Bindi).

In either way, to date three natural QCs are known from the Khatyrka meteorite. In meteorite research the mineral assemblage can aid understanding of the formation condition of an associated phase; however, the proper interpretation demands a laboratory-controlled synthesis. Hu et al. apply recent advances in the Graded Density Impactor fabrication technique (Kelly et al., 2019) to shock-synthesize i-phase II. The authors use a special Al–Cu–W disk in an Fe-bearing 304 stainless-steel target chamber and perform two experiments corresponding to an estimated peak shock pressure of 20–30 GPa for 800 ns and 30–35 GPa for 600 ns, respectively. The careful sample characterization, including the state-of-the-art electron backscattered diffraction method, reveals the first experiment (Fig. 1) resulted in coexisting intermetallic phases of i-phase II, stolperite (β, AlCu) + khatyrkite (θ, Al₂Cu), which perfectly matches with the assemblage found in the Khatyrka meteorite. The second experiment shows the formation of a rather Fe-rich quinary i-phase (Al_68.6Fe_14.5Cu_11.2Cr₄Ni_1.8), together with stolperite (β, AlCu) and hollisterite (λ, Al₁₃Fe₄).

A key finding of Hu et al. is the shock-synthesized i-phase II, because it represents the first example of a quasicrystal composition discovered in nature prior to being synthesized in the laboratory. Although i-phase I (icosahedrite) together with the d-phase (decagonite) were previously produced by Al-alloy quenching experiments and reported to be thermodynamically stable with a very narrow range of composition (Tsai et al., 1987), such laboratory conditions were likely inconsistent with those experienced by the Khatyrka meteorite. Furthermore, the previous Al-alloy quenching experiments could not explain the stability of i-phase II and its relationship to i-phase I. Now the authors’ findings provide unique insights into the intricate details of the Al–Cu–Fe phase diagram. In particular, they suggest the thermodynamically stable Al₆₃Cu₂₄Fe₁₃ phase could separate into two disconnected fields under shock pressure above 20 GPa, leading to the co-existence of Fe-rich (i-phase I) and Fe-poor (i-phase II) QCs consistent with the previous findings of the Khatyrka meteorite (Bindi et al., 2016).

QC formation requires controlled syntheses including rapid quenching, during which unusual crystal nucleation and growth can be favoured. The new findings reported by Hu et al. demonstrate that shock-recovery experiments provide a novel strategy for preparing and exploring this exciting material group.

References

Bindi, L., Lin, C., Ma, C. & Steinhardt, P. J. (2016). Sci. Rep. 6, 38117.

Bindi, L., Steinhardt, P. J., Yao, N. & Lu, P. J. (2009). Science, 324, 1306–1309.

Bindi, L., Yao, N., Lin, C., Hollister, L. S., Andronicos, C. L., Distler, V. V., Eddy, M. P., Kostin, A., Kryachko, V., MacPherson, G. J., Steinhardt, W. M., Yudovskaya, M. & Steinhardt, P. J. (2015). Sci. Rep. 5, 9111.

Hu, J., Asimov, P. D., Ma, C. & Bindi, L. (2020). IUCrJ, 7, 434–444.

Kelly, J. P., Nguyen, J. H., Lind, J., Akin, M. C., Fix, B. J., Saw, C. K., White, E. R., Greene, W. O., Asimow, P. D. & Haslam, J. J. (2019). J. Appl. Phys. 125, 145902.

Lifshitz, R. (2003). Found. Phys. 33, 1703–1711.

Lord, E. A., Ranganathan, S. & Kulkarni, U. D. (2000). Curr. Sci. 78, 6472.

Pauling, L. (1985). Nature, 317, 512–514.

Prodan, A., Hren, R. D., van Midden, M. A., van Midden, H. J. P. & Zupanic, E. (2017). Sci. Rep. 7, 12474.

Shechtman, D., Blech, I., Gratias, D. & Cahn, J. W. (1984). Phys. Rev. Lett. 53, 1951–1953.

Tsai, A. P., Inoue, A. & Masumoto, T. (1987). Jpn. J. Appl. Phys. 26, L1505–L1507.

This article was originally published in IUCrJ (2020). 7, 368–369.

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Meeting report (IUCr supported)

ECM32 Satellite Meeting: Mathematical and Theoretical Crystallographic Workshop
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ECM32 Satellite Meeting: Mathematical and Theoretical Crystallographic Workshop

Massimo NespoloBernd SouvignierBerthold Stöger

Ahead of the ECM32 meeting, hosted by the University of Vienna, Austria, numerous satellite workshops were held at the TU (Technical University) Wien. Most took place in the electrical engineering building with shared coffee and lunch breaks. Within this scope, the IUCr Commission on Mathematical and Theoretical Crystallography (MaThCryst) organized a 2.5 day satellite workshop, from 17 to 19 August 2020, with a special focus on graph theory and modular structures.

Fifteen participants from diverse backgrounds (chemistry, mathematics and crystallography) attended the workshop. The participants hailed from six countries: Austria, Germany, Israel, Japan, Russia and the UK.

On the first day, fundamentals of graph theory and their applications to crystal structure analysis were presented by Bernd Souvignier (Radboud University Nijmegen, Netherlands). Special focus was placed on the analysis of periodic nets. These are crucial to describe the connectivity of atoms or groups in crystalline materials. In the morning session of the second day, Massimo Nespolo (Université de Lorraine, Nancy, France) introduced the application of space groupoids to describe modular structures in a general way. In modular structures, which are ubiquitous in all classes of materials, operations are applied to subspaces of crystal space. These substructures can be non-periodic blocks or sub-periodic units (rods or layers). As the operations relating two modules need not apply to the whole crystal, their composition forms a groupoid instead of a group. In the afternoon Berthold Stöger (Technical University Vienna, Austria) focused on the concrete case of order–disorder (OD) structures. These are modular structures composed of layers that are arranged in such a way that there is only one geometrical way of placing adjacent layers. Thus, an infinity of different stacking arrangements, which are nevertheless locally equivalent, can exist, leading to challenging problems such as twinning or disorder. The sessions on graph theory and modular structures comprised approximately two thirds lecture and one third exercises, including discussion.

In the morning session of the last day, the session on OD structures was completed and two oral talks of ca 30 minutes were given by two attendees. Shelomo I. Ben-Abraham (Beer-Sheba, Israel) presented Multidimensional crossed cube tilings. Vitaliy Kurlin (Liverpool, UK) in his talk How to correctly sample unit cells in computer simulations of crystal structures proposed using Wigner–Seitz cells instead of reduced cells to provide a unique and continuous mapping of lattice metrics. The talks resulted in a lively discussion. The workshop closed during lunch of 19 August with a poster presentation by three attendees.

On the evening of the second day the participants of all workshops met at a typical Viennese “Heuriger” to enjoy local food and wine. This social evening provided a unique networking opportunity.

Four young participants (two male and two female) from three countries (UK, Germany and Russia) applied for travel assistance, which was generously provided by the IUCr.

The feedback was generally positive. Unifying participants from such diverse backgrounds was challenging, but ultimately satisfying. The organizers and participants published six papers in the May 2020 special issue of Crystal Research and Technology on Mathematical Crystallography 2019. Owing to the positive experience, the organizers plan to repeat workshops on mathematical and theoretical crystallography at upcoming ECMs.

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Meeting report (IUCr supported)

Fourth International Workshop on X-ray Crystallography in Structural Biology
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Fourth International Workshop on X-ray Crystallography in Structural Biology

Maqsood Ahmed

The Fourth International Workshop on X-ray Crystallography in Structural Biology was held at the Islamia University of Bahawalpur, Pakistan, from 25 to 27 February 2020. The first meeting in this series was held at the National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, in November 2015; the second at FC College University Lahore in October 2016; and the third at the International Centre for Chemical and Biological Sciences (ICCBS), University of Karachi, in 2018. The aim of these workshops is to build capacity in the area of structural biology, which has had a very late start in Pakistan but is now gaining ground. As with the previous meetings, the fourth workshop was sponsored by the IUCr. Additional financial support was provided by the Pakistan Science Foundation (PSF), the Higher Education Commission of Pakistan. The Islamia University of Bahawalpur provided complete logistical support. Bruker Corporation and Douglas Instruments provided significant sponsorship.

Group photo.

Bahawalpur was chosen as the venue for the fourth workshop for multiple reasons. It has a unique landscape with the Cholistan Desert on one side and agricultural fields on the other. The city is famous for its palaces, which were built by the Nawabs of Bahawalpur. It is located almost in the centre between Karachi and Islamabad. The city has three universities. It is easily accessible from other large cities like Multan, Lahore and Faisalabad through a network of motorways and also has its own airport. And above all, the Islamia University of Bahawalpur has recently established a Materials Chemistry Laboratory that hosts a dual-source single-crystal X-ray diffractometer and a powder X-ray diffractometer. This lab is now regularly publishing research on small molecules and seriously wanted to undertake structural biology.

Opening ceremony.

To provide high-quality hands-on training with a high student-to-teacher ratio, renowned structural biologists from abroad and from within Pakistan were invited. Samar Hasnain (University of Liverpool UK), Elspeth Garman (University of Oxford, UK), Richard Garratt (University of Sao Paolo, Brazil; sponsored by the IUCr) and Osman Asghar Mirza (University of Copenhagen, Denmark) carefully designed courses over the span of three days. They were assisted by national experts.

There were around 70 participants of which more than half were female. The participants were mainly Master’s or PhD students. The IUCr sponsored full economy class travel and lodging for 3 nights for 40 young scientists from across Pakistan. This support from the IUCr to young scientists proved crucial for the success of the workshop as the most serious participants from the disciplines of chemistry, physics, biotechnology, medicine and agriculture were able to participate.

Each day started with one or two comprehensive lectures. In his plenary lectures, Professor Hasnain gave an extensive overview of hot topics in structural biology, which the audience found very inspiring, and Professor Garratt nicely explained the basic concepts of symmetry and diffraction. The participants were divided into three groups and parallel sessions were organized. The participants received hands-on training in all aspects of protein structure determination including expression, purification, crystallization and data collection on the newly installed Bruker D8 Venture diffractometer equipped with an Oxford Cryosystems Cobra cryosystem. Moaz-ur-Rehman, Ahmed Akram, Muhammad Imran and Amir Shehzad conducted tutorials on expression and purification of proteins. Professor Garman and Maqsood Ahmed provided extensive hands-on training on harvesting the crystals under an Olympus SZX10 polarizing microscope equipped with a high-resolution DP74 camera. The students learnt how to mount the crystals on the goniometer head and visualize the diffraction. Lengthy sessions on data processing and model building using CCP4 and COOT were organized on the second and third days. Professor Garman prepared the course material on CCP4, and Dr Mirza, Malik Muhammad Shoaib and Saima Rasheed conducted the tutorials on refinement and model building.

Hands-on training. Left: protein expression and purification; right: crystal hunting and the single-crystal X-ray diffractometer.

On the final day of the workshop, the participants were required to take a written examination, which focused on the activities of the three days. Most of the participants fared very well. Prizes provided by Bruker were distributed among the top five scorers.

Each day the participants were served with lunch and dinner. An elegant gala dinner was hosted on the evening of the second day on the lawns of the beautiful Noor Mahal, where the participants admired the light show.

The opening and closing ceremonies were presided over by the Vice Chancellor of the Islamia University of Bahawalpur who took a keen interest in the event and offered his full support to efforts to promote structural biology in Bahawalpur.

A one-day sightseeing trip was organized on the next day of the workshop. The participants visited the historical Sadiq Garh Palace and the Derawar Fort in the Cholistan Desert. The participants also had a guided tour of the Biodiversity Park of the Islamia University of Bahawalpur situated in the Cholistan Desert.

Elspeth Garman and Richard Garratt enjoying a camel ride at Derawar Fort.

The event gained extensive coverage in newspapers and on television. Additional photos can be seen here.

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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.

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