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IUCr Congress collection
Celebrating the 75th Anniversary of the IUCr
The triennial congresses of the IUCr are the major international scientific meetings for structural scientists worldwide. This virtual issue presents a collection of articles covering research reported at the 26th IUCr Congress and articles celebrating the 75th Anniversary of the IUCr. The 26th Congress was held in Melbourne, Australia from 22 to 29 August 2023. Articles will be added to the collection during 2023 and 2024.
editorial
The International Union of Crystallography (IUCr) and its journals are celebrating their 75th anniversary. In this editorial, some of the publication achievements are highlighted and prospects for the future reviewed in an emerging open-access world.
lead articles
This article reviews phase evaluation in macromolecular crystallography. It accompanies the 2023 Ewald Prize lecture at the 26th IUCr Congress, paying tribute to Paul Ewald's far-reaching influence.
feature articles
Interoperability of scientific data within crystallography has been achieved to a high level by the adoption of standard exchange formats and protocols. Extending such interoperability across other disciplines is a goal of the International Science Council Committee CODATA, to which the IUCr has been a leading contributor. Our article combines a description of the importance of interoperability for addressing grand challenges with a desire to stimulate the crystallographic community to continue exploring this topic.
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Structural sciences serve as a bridge between the fundamental understanding of materials and their applications, by elucidating the atomic and molecular intricacies that define the performance of functional materials. Spanning diverse fields, from energy storage to catalysis, this article emphasizes the evolving experimental techniques that have revolutionized our knowledge of structures and dynamic processes, positioning structural science as the essential guide to the future development of functional materials.
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Since they do not belong to the class of subperiodic groups, line groups thus far have been beyond the scope of symmetries traditionally studied in crystallography, although they describe the symmetry of numerous `one-dimensional' crystals (i.e. monoperiodic structures). Therefore, together with an overview of frieze, rod and layer groups, a brief introduction to line groups is presented.
This paper proposes a rigorous definition of a periodic structure as an equivalence class of periodic sets under rigid motion, which is a composition of translations and rotations.
The 26th IUCr congress held in Melbourne brought discussions on micro-crystallization and in vivo crystallography within structural biology to the forefront, highlighting innovative approaches and collaborative efforts to advance macromolecular research.
Using synchrotron radiation, diffraction data extending to 0.70 Å resolution were collected from crystals of the small protein crambin at room temperature (297 K), and the structure was refined with spherical-atom approximation to an R factor of 0.0591, revealing (i) protein regions with multiple conformations, (ii) extended water networks correlated with protein conformations and (iii) minimal radiation damage. The structure sets a standard for room-temperature refinement of macromolecular targets and provides accurate data for modeling protein–solvent interactions.
PDB reference: ultrahigh-resolution crambin RT structure, 9ewk
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This article gives an overview of current trends and challenges in serial crystallography, with a focus on results from time-resolved experiments.
topical reviews
The RCSB PDB research-focused web portal at https://www.rcsb.org/ provides important tools and resources to search, visualize and analyze experimentally determined 3D biostructures alongside computed structure models of proteins predicted using artificial intelligence/machine-learning based tools.
This topic review summarizes structures of chaperones complexed with MHC-I, the structural principles that govern peptide exchange and the mechanism in antigen presentation.
Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. This article presents recent progress in the structural analysis of FDHs together with their potential biotechnological applications.
Photosystem II is the enzyme responsible for generating nearly all the oxygen in the atmosphere. Room-temperature time-resolved crystallography and spectroscopy measurements at X-ray free-electron lasers help to elucidate the sequence of events in the water oxidation reaction of photosystem II leading to the formation of dioxygen from two molecules of water.
Diffuse X-ray scattering is used to characterize the time dependence of the liquid phase emerging from femtosecond laser-induced melting of polycrystalline gold thin films using an XFEL. Its structure factor and partial pair distribution function confirm the liquid origin of the diffuse scattering. The liquid fraction increases with a characteristic rise-time of 13 ps.
Platinum(II) complexes exhibit intense luminescence based on their molecular arrangement and chromic luminescence, which is a color change in response to gentle stimuli such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively control the chromic phenomenon of platinum(II) complexes.
In structural biology, the analogy of a key (ligand) fitting a lock (protein) is commonly used to describe the binding process. In this context, we illustrate the evolutionary development of diverse locks that exhibit specific binding to a shared key: Neu5Ac. The intricate specificity of the interaction between various locks and the common key (Neu5Ac) is explored in our review.
Bridging length scales in hard materials with ultra-small angle X-ray scattering – a critical review
This review examines the use of ultra-small angle X-ray scattering (USAXS), a nondestructive technique for analyzing the multi-scale microstructures of hard materials such as ceramics, metals and composites. It discusses the principles, benefits and challenges of USAXS, along with its potential to advance materials development and optimize manufacturing processes, while also considering future enhancements through multimodal characterization and machine learning.
The TIR (Toll/interleukin-1 receptor) domains are found in proteins with roles in the immune systems of humans, plants and bacteria. A combination of structural methods ranging from X-ray and electron crystallography to cryogenic electron microscopy and nuclear magnetic resonance spectroscopy has been required to understand how these domains contribute to signalling, highlighting the complementarity of different structural approaches.
Biological materials obtain their properties through hierarchical structuring. Understanding such materials calls for multimodal and multiscale approaches. Based on two example systems, bone and shell, we discuss current analytical approaches, their capabilities and limits, and how to tie them together to fully cover the different length scales involved in understanding materials' functions. We will further discuss advances in this area and future developments, the possible roadblocks (radiation damage, data quantity, sample preparation) and potential ways to overcome them.
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This topical review discusses the recent progress in low-dose high-resolution imaging of metal–organic framework materials and gives a brief outlook on possible future directions.
The electric field responses of the average and local lattice strains and polar nanoregions of relaxor ferroelectric PMN-30PT single crystals were revealed by multi-scale and time-resolved X-ray diffraction under DC and AC electric fields.
This review summarizes the methodological aspects of laboratory X-ray powder micro-diffraction and demonstrates the assets of the method in the research of painted artworks for evaluation of their provenance or diagnosing their degradation.
research letters
In this work, a reversible non-invasive light-induced mesophase transition from lamellar to cubic Pn3m is observed in mixed azobenzene-lipid and phospholipid vesicles using small-angle X-ray scattering.
research articles
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A binding approach based on electronic force density fields was used to describe the structures of the molecule, dimer and crystal of a uracil derivative. Transferable multipole pseudo-atoms were successfully used to reconstruct the inner-crystal electronic force density fields.
CCDC reference: 2259862
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AlphaFold predictions can be used both as a starting point for structure determination and as a method of model optimization. The Phenix PredictAndBuild tool automates iterative prediction and model building, yielding a density map and model starting with sequence information and crystallographic data.
This contribution outlines how to obtain perfect precise colorings of tilings, and illustrates this by obtaining perfect precise colorings of some families of k-valent semiregular planar tilings with k colors.
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Advances in X-ray hardware and software have revolutionized crystallography: now crystal structures can be routinely solved first, with publication-quality datasets collected second. This same approach now allows multi-grain crystallography to be completed in the laboratory with Cu Kα X-rays.
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All the possibilities for permissible (mismatch-free) walls between monoclinic domains of pseudocubic ferroic perovskites are analyzed. Analytical expressions are derived for the orientation of such walls, the orientation relationship between the lattice vectors and the separation between Bragg peaks diffracted from matched domains.
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Following the previous work [Biran & Gorfman (2024). Acta Cryst. A80, 112–128], all the possibilities for permissible (mismatch-free) walls between monoclinic domains of pseudocubic ferroelectric perovskites of MC type are analyzed. The study yields analytical expressions for the orientation of such walls, the orientation relationship between the lattice vectors and for the separation between Bragg peaks diffracted from matched domains.
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X-ray absorption spectroscopy (XAS) measurements of N-truncated amyloid-β samples were corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumbers k, permitting hypothesis testing in structural refinements. A new protocol was developed using extended X-ray absorption fine structure data analysis for monitoring radiation damage in real time and post-analysis.
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A dipropyl-substituted isoindigo derivative has three polymorphs with different molecular conformations and arrangements.
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A single-particle structure determination pipeline is implemented in the open-source software xFrame, which includes methods for determining rotational invariants from X-ray scattering patterns and performing structure reconstructions by iterative phasing of rotational invariants.
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A simple symmetric 2D scan using a point focus beam was used to determine the fibre axis of fibre-textured satin spar samples. A geometric explanation of the `wing' feature formed by the diffraction spots in 2D scans helps to visualize the nature of the reciprocal layers of the fibre-textured samples through wide-range reciprocal space mapping.
The 3N-dimensional maxima of the square of the wavefunction, the so-called Born maxima, show beyond doubt that the electronic structure of atoms persists in molecules, either in their original ground state or some low-lying excited state. The electron density is only a low-dimensional projection of this much richer landscape.
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The disequilibrium Sn content in Pb inclusions present in ancient (Sn,Cu)-bronze samples may in principle be used for authentication purposes. The present article explores the applicability of a method based on precise diffraction measurement of the Pb lattice parameter.
Rational drug discovery and design require a deep understanding of the structure and thermodynamics of protein–ligand interactions. Here, the human carbonic anhydrase family of enzymes and their specific sulfonamide ligands are used to describe binding assays and crystal structures for understanding of protein–compound recognition principles.
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A new polymorph of 1,3-diacetylpyrene that is luminescent in the solid state and a prominent negative thermal expansion material has been obtained from its melt. A thorough structural characterization of this new crystal form was performed in a wide temperature and pressure range using single-crystal X-ray diffraction. Structural studies have been combined with steady-state UV–Vis spectroscopy and periodic density functional theory calculations. A previously published methodology of crystal placement in a diamond anvil cell has been successfully applied in predicting optimal 2°AP-β sample orientation, ensuring >80% data coverage and enabling unrestrained Hirshfeld atom refinements for high-pressure structures as well as analysis of anharmonic oscillations.
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Full pattern analyses of small-angle X-ray and neutron scattering data with both discrete reflections and central diffuse scattering are presented. Data with both equatorial streaks and two- and four-point reflections can be fitted in elliptical coordinates with relatively few parameters.
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Laboratory powder diffraction and microtomography techniques are sequentially used in the same volume of the same sample to study the process of cement hydration with time.
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This paper demonstrates an event-mode imaging based neutron diffraction detector system that employs a scintillator screen, an image intensifier and a Timepix3-based camera. This highly configurable approach allows for large-solid-angle low-cost neutron diffraction setups with a performance comparable to that of the 3He detectors on a time-of-flight neutron diffraction beamline.
Consensus small-angle X-ray scattering (SAXS) data from five proteins in solution, generated from 171 independent measurements on 12 beamlines using a maximum likelihood method, are used to benchmark computational methods for predicting SAXS profiles from atomic coordinates. The results reveal important strengths and limitations of different methods that are serving a growing community of users in applications ranging from fundamental integrative structural biology to drug discovery and development.
SASBDB references: ribonuclease A, SASDUA4; urate oxidase, SASDUB4; xylose isomerase, SASDUC4; xylanase, SASDUD4; lysozyme, SASDUE4
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This paper describes real-time statistical analysis of liquid jet images for serial femtosecond crystallography (SFX) experiments at the European XFEL. This analysis forms one part of the automated jet realignment system for SFX experiments at the SPB/SFX instrument of the European XFEL.
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This study addresses the structural basis of TIR-domain-mediated signal transduction in Toll-like receptor 2 pathways. It is demonstrated that TLR2, but not TLR1 or TLR6, TIR domains induce the formation of MyD88 TIR-domain assemblies in vitro. The MicroED structure of TLR2-induced MyD88 TIR assemblies determined at 2.85 Å resolution highlights conformational changes that are crucial for signaling and provides evidence that TLR2 can directly interact with MyD88 to initiate TLR signaling.
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Successful crystallographic structure-based drug-discovery (SBDD) support of early-stage pharmaceutical research programs requires the timely establishment of a robust crystallization system for the target protein. This enables structure determination of early high-throughput screening or fragment-screening hits, in turn maximizing the impact of SBDD on hit optimization. Here, a collection of complementary case studies are presented that demonstrate typical strategies to achieve this goal.
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The HEIDI experiment-management platform supports high-throughput fragment screening and facilitates structure-based research, design and drug discovery by both academic and industrial users at the Swiss Light Source crystallization facility and macromolecular crystallography beamlines. Collectively, the software solutions streamline sample preparation, beamline data acquisition and data processing, and facilitate fully automated experiments.
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The behavior of iterative projection algorithms for crystallographic phase retrieval is systematically investigated. It is shown that information present in the algorithm trajectory following convergence can be exploited to improve the final density estimate.
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Histidine protonation is fraught, but a new quantum-mechanical method can provide insight into choices.
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A sample- and time-efficient method to obtain serial crystallography data from batch-grown microcrystals dispensed as drops on a 96-well crystallization plate is described. This offers a versatile method to obtain low-dose room-temperature structures and guide the optimization of microcrystallization for synchrotron and XFEL serial crystallography experiments.
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This study highlights the efficiency and effectiveness of small-wedge synchrotron crystallography in analyzing protein structures through massive data collection and advanced data-processing techniques, including machine learning, resulting in significant improvements in structural information.
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A crystallographic and biochemical study of the M405S variant of D. vulgaris formate dehydrogenase AB is reported in order to clarify the role of Met405 in catalysis in an enzyme that has applications in climate-change mitigation tools.
teaching and education
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Most introductions to the topic of crystallography only occur during tertiary education, which presents a challenge to communicating it to wider groups. This work describes a simple activity targeted at classroom and community audiences to demonstrate crystal structure(s) and the wider impact of crystallography.
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In crystallography there exist a wide variety of online resources such as web pages, interactive applets, databases and programs that can be implemented in both virtual and traditional classrooms. Among these, the Bilbao Crystallographic Server, the Cambridge Structural Database, Mercury, VESTA and Jmol are highlighted for teaching fundamental crystallography since they are useful resources for crystallographic symmetry handling and visualization.
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Animations, videos and 3D models have been designed to visualize the effects of symmetry operators on selected cases of crystal structures, pointing out the relationship with the diagrams published in International Tables for Crystallography, Vol. A.
research communications
The Young Crystallographers were founded in 2013 within the German Crystallographic Association and have revitalized the field of crystallography by establishing collaboration and support among early career researchers, organizing educational events, and promoting scientific contributions on national and international stages.
short communications
Annealing-induced structural transformations in titanium–chromium oxide crystals potentially highlight a role in modulating thermal conductivity through the regularization of crystallographic shear plane spacing.
computer programs
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A program has been developed to assist researchers interested in bending crystals to evaluate crystal deformation from a single optical image.
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A Python-based software package is presented that can compute the pair angle distribution function from X-ray or electron fluctuation scattering data of disordered materials.
letters to the editor
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The formal launch of Protein Data Bank China (PDBc) is announced, and the history of the wwPDB, recently established mechanisms for adding new wwPDB data centers and the processes developed to bring PDBc into the partnership are described.
