The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallo­graphic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.

Preparation of biomacromolecules for structural biology studies is a complex and time-consuming process. The goal is to produce a highly concentrated, highly pure product that is often shipped to large facilities with tools to prepare the samples for crystallization trials or for measurements at synchrotrons and cryoEM centers. The aim of this article is to provide guidance and to discuss general considerations for shipping biomacromolecular samples. Details are also provided about shipping samples for specific experiment types, including solution- and cryogenic-based techniques. These guidelines are provided with the hope that the time and energy invested in sample preparation is not lost due to shipping logistics.

Brucella ovis is an etiologic agent of ovine epididymitis and brucellosis that causes global devastation in sheep, rams, goats, small ruminants and deer. There are no cost-effective methods for the worldwide eradication of ovine brucellosis. B. ovis and other protein targets from various Brucella species are currently in the pipeline for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), with the aim of identifying new therapeutic targets. Furthermore, the wealth of structures generated are effective tools for teaching scientific communication, structural science and biochemistry. One of these structures, B. ovis leucine-, isoleucine-, valine-, threonine- and alanine-binding protein (BoLBP), is a putative periplasmic amino acid-binding protein. BoLBP shares less than 29% sequence identity with any other structure in the Protein Data Bank. The production, crystallization and high-resolution structures of BoLBP are reported. BoLBP is a prototypical bacterial periplasmic amino acid-binding protein with the characteristic Venus flytrap topology of two globular domains encapsulating a large central cavity containing the peptide-binding region. The central cavity contains small molecules usurped from the crystallization milieu. The reported structures reveal the conformational flexibility of the central cavity in the absence of bound peptides. The structural similarity to other LBPs can be exploited to accelerate drug repurposing.

Crystallographic fragment screening has become a pivotal technique in structure-based drug design, particularly for bacterial targets with a crucial role in infectious disease mechanisms. The enzyme CdaA, which synthesizes an essential second messenger cyclic di-AMP (c-di-AMP) in many pathogenic bacteria, has emerged as a promising candidate for the development of novel antibiotics. To identify crystals suitable for fragment screening, CdaA enzymes from Streptococcus pneumoniae, Bacillus subtilis and Enterococcus faecium were purified and crystallized. Crystals of B. subtilis CdaA, which diffracted to the highest resolution of 1.1 Å, were used to perform the screening of 96 fragments, yielding data sets with resolutions spanning from 1.08 to 1.87 Å. A total of 24 structural hits across eight different sites were identified. Four fragments bind to regions that are highly conserved among pathogenic bacteria, specifically the active site (three fragments) and the dimerization interface (one fragment). The coordinates of the three active-site fragments were used to perform an in silico drug-repurposing screen using the OpenEye suite and the DrugBank database. This screen identified tenofovir, an approved drug, that is predicted to interact with the ATP-binding region of CdaA. Its inhibitory potential against pathogenic E. faecium CdaA has been confirmed by ITC measurements. These findings not only demonstrate the feasibility of this approach for identifying lead compounds for the design of novel antibacterial agents, but also pave the way for further fragment-based lead-optimization efforts targeting CdaA.

Glucose-6-phosphate dehydrogenase (G6PD) is the first enzyme in the pentose phosphate pathway. It has been extensively studied by biochemical and structural techniques. 13 X-ray crystal structures and five electron cryo-microscopy structures in the PDB are focused on in this topical review. Two F420-dependent glucose-6-phosphate dehydrogenase (FGD) structures are also reported. The significant differences between human and parasite G6PDs can be exploited to find selective drugs against infections such as malaria and leishmaniasis. Furthermore, G6PD is a prognostic marker in several cancer types and is also considered to be a tumour target. On the other hand, FGD is considered to be a target against Mycobacterium tuberculosis and possesses a high biotechnological potential in biocatalysis and bioremediation.

Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9–5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.

Plasmodium vivax is a major cause of malaria, which poses an increased health burden on approximately one third of the world's population due to climate change. Primaquine, the preferred treatment for P. vivax malaria, is contraindicated in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency, a common genetic cause of hemolytic anemia, that affects ∼2.5% of the world's population and ∼8% of the population in areas of the world where P. vivax malaria is endemic. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) conducted a structure–function analysis of P. vivax N-myristoyltransferase (PvNMT) as part of efforts to develop alternative malaria drugs. PvNMT catalyzes the attachment of myristate to the N-terminal glycine of many proteins, and this critical post-translational modification is required for the survival of P. vivax. The first step is the formation of a PvNMT–myristoyl–CoA binary complex that can bind to peptides. Understanding how inhibitors prevent protein binding will facilitate the development of PvNMT as a viable drug target. NMTs are secreted in all life stages of malarial parasites, making them attractive targets, unlike current antimalarials that are only effective during the plasmodial erythrocytic stages. The 2.3 Å resolution crystal structure of the ternary complex of PvNMT with myristoyl-CoA and a novel inhibitor is reported. One asymmetric unit contains two monomers. The structure reveals notable differences between the PvNMT and human enzymes and similarities to other plasmodial NMTs that can be exploited to develop new antimalarials.

Guanosine 5'-monophosphate (GMP) synthetase (GuaA) catalyzes the last step of GMP synthesis in the purine nucleotide biosynthetic pathway. This enzyme catalyzes a reaction in which xanthine 5'-monophosphate (XMP) is converted to GMP in the presence of Gln and ATP through an adenyl-XMP intermediate. A structure of an XMP-bound form of GuaA from the domain Bacteria has not yet been determined. In this study, the crystal structure of an XMP-bound form of GuaA from the thermophilic bacterium Thermus thermophilus HB8 (TtGuaA) was determined at a resolution of 2.20 Å and that of an apo form of TtGuaA was determined at 2.10 Å resolution. TtGuaA forms a homodimer, and the monomer is composed of three domains, which is a typical structure for GuaA. Disordered regions in the crystal structure were obtained from the AlphaFold2-predicted model structure, and a model with substrates (Gln, XMP and ATP) was constructed for molecular-dynamics (MD) simulations. The structural fluctuations of the TtGuaA dimer as well as the interactions between the active-site residues were analyzed by MD simulations.

Proliferating cell nuclear antigen (PCNA) plays a critical role in DNA replication by enhancing the activity of various proteins involved in replication. In this study, the crystal structure of ApePCNA1, one of three PCNAs from the thermophilic archaeon Aeropyrum pernix, was elucidated. ApePCNA1 was cloned and expressed in Escherichia coli and the protein was purified and crystallized. The resulting crystal structure determined at 2.00 Å resolution revealed that ApePCNA1 does not form a trimeric ring, unlike PCNAs from other domains of life. It has unique structural features, including a long interdomain-connecting loop and a PIP-box-like sequence at the N-terminus, indicating potential interactions with other proteins. These findings provide insights into the functional mechanisms of PCNAs in archaea and their evolutionary conservation across different domains of life. A modified medium and protocol were used to express recombinant protein containing the lac operon. The expression of the target protein increased and the total incubation time decreased when using this system compared with those of previous expression protocols.

The crystal structure of the intracellular domain of transforming growth factor β type I receptor (TβR1) in complex with the competitive inhibitor SB505124 is presented. The study provides insights into the structure and function of TβR1 in complex with SB505124, and as such offers molecular-level understanding of the inhibition of this critical signalling pathway. The potential of SB505124 as an avenue for therapy in cancer treatment is discussed on basis of the results.

Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical techniques with calibration standards, cryoEM has lacked comprehensive biological test samples. Here, a cryoEM calibration sample consisting of a mixture of compatible macromolecules is introduced that can not only be used for resolution optimization, but also provides multiple reference points for evaluating instrument performance, data quality and image-processing workflows in a single experiment. This combined test specimen provides researchers with a reference point for validating their cryoEM pipeline, benchmarking their methodologies and testing new algorithms.

The reciprocal of a non-primitive unit cell is not a unit cell and the basis vectors do not correspond to cell lengths.

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.

Fixed targets (`chips') offer efficient, high-throughput microcrystal delivery for serial crystallography at synchrotrons and X-ray free-electron lasers (XFELs). Within this family, sheet-on-sheet (SOS) chips offer noteworthy advantages in cost, adaptability, universality and ease of crystal loading. We describe our latest generation of SOS devices, which are now in active use at both synchrotrons and XFELs.

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.

This study validates the feasibility of applying a smearing method for the multi-slit very small angle neutron scattering instrument (MS-VSANS) at the China Spallation Neutron Source. Through analysis limited to a vertical range of 8 mm, the study demonstrates consistency between the predicted smearing function and experimental data, marking a significant milestone in utilizing real data from such instruments.

Direct measurements have been taken of nanoscale domain structure in ferroelectric lead zirconate titanate around a grain boundary. Characterizing the evolution of this structure under an electric field is critical for predicting dielectric and piezoelectric response.

The growth quality of AlN single crystals was improved by optimizing the crucible structure for Al vapor transport with the help of finite element simulation.

We present a demonstration of high-pressure grazing-incidence small-angle neutron scattering for soft matter thin films. The results suggest changes in water reorganization at different pressures.

The correct determination of X-ray transmission at X-ray nanoprobes equipped with small beamstops for small- and wide-angle X-ray scattering collection is an unsolved problem with huge implications for data correction pipelines. We present a cost-effective solution to detect the transmission via the X-ray fluorescence of the beamstop with an avalanche photodiode.

New software capabilities in RMCProfile allow researchers to study the structure of materials by combining machine learning interatomic potentials and reverse Monte Carlo.

Rotations of small- and wide-angle X-ray scattering samples during acquisition are shown to give a drastic improvement in the reliability of the characterization of anisotropic precipitates in metallic alloys.

A symmetry guide for the secondary structural degrees of freedom and related physical properties generated by tilts of BX6 octahedra in perovskites is proposed.

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.

AnACor2.0 significantly accelerates the calculation of analytical absorption corrections in long-wavelength crystallography, achieving up to 175× speed improvements. This enhancement is achieved through innovative sampling techniques, bisection and gridding methods, and optimized CUDA implementations, ensuring efficient and accurate results.

The effect of boron in BxGa1−xN/SiC heteroepitaxy was established by X-ray diffraction reciprocal-space maps on symmetric 0002 and asymmetric 11 {overline 2} 4 reflections. The density of screw and edge threading dislocations was quantified in the framework of the mosaic model.

A new processing technique for synchrotron scanning 3D X-ray diffraction data is introduced, utilizing symmetric Bragg reflections hkl and hkl, known as Friedel pairs. This technique is designed to tackle the difficulties associated with large, highly deformed, polyphase materials, especially geological samples.

This study examines the quality of charge density obtained by fitting the multipole model to wavefunctions in different basis sets. The complex analysis reveals that changing the basis set quality from double- to triple-zeta can notably improve the charge density related properties of a multipole model.

This paper describes real-time statistical analysis of liquid jet images for SFX experiments at the European XFEL. This analysis forms one part of the automated jet re-alignment system for SFX experiments at the SPB/SFX instrument of European XFEL.

A neutron far-field interferometer is under development at NIST with the aim of enabling a multi-scale measurement combining the best of small-angle neutron scattering (SANS) and neutron imaging and tomography. We use the close relationship between SANS, ultra-SANS, spin-echo SANS and dark-field imaging and measurements of monodisperse spheres as a validation metric, highlighting the strengths and weaknesses of each of these neutron techniques.

Here, an open-source Python library for identifying and screening potential stacking fault models in crystalline materials with planar disorder is presented.

The performance of a high-Z photon-counting detector for powder diffraction measurements at high (>50 keV) energies is characterized, and the appropriate corrections are described in order to obtain data of higher quality than have previously been obtained from 2D detectors in these energy ranges.

Combined 100 ms resolved grazing-incidence small/wide-angle X-ray scattering and optical interferometry reveal that the additive diiodooctane can significantly double the solvent evaporation rate, thereby effectively suppressing the rapid spinodal decomposition process in the early stage of spin-coasting, favouring slow phase segregation kinetics with nucleation and growth.

The position- and time-resolved monitoring of a mechanochemical reaction using synchrotron powder X-ray diffraction revealed a position-independent increase rate of product in the jar of a shaker mill.

The article presents a non-invasive nanoscale imaging technique that can be used in screening crystallization conditions for protein micro- and nanocrystals.

RAPID (RAtio method Pattern InDexing) is an ImageJ macro script developed for the quick determination of sample orientation and indexing of calibrated and uncalibrated zone axis aligned electron diffraction patterns from materials with a cubic crystal structure. In addition to SAED and NBED patterns, the program is also capable of handling zone axis TEM Kikuchi patterns and FFTs derived from HR(S)TEM images. The software enables users to rapidly determine whether materials are cubic, pseudo-cubic, or non-cubic, and to distinguish between P, I, and F Bravais lattices. It can also provide lattice parameters for material verification and aid in determining the camera constant of the instrument, thus making the program a convenient tool for on-site crystallographic analysis in the TEM laboratory.

This study proposes an operation optimization framework for impurity-free recycling of spent lithium-ion batteries. Using a hybrid population balance equation integrated with a data-driven condition classifier, the study firstly identifies the optimal batch and semi-batch operation conditions that significantly reduce the operation time with 100% purity of product; detailed guidelines are given for industrial applications.

The L-edge EXAFS of the entire set of lanthanide oxides were collected and modeled, taking into consideration the aggregation of inequivalent absorbing sites, geometric parameterization of the crystal lattice and multielectron excitation removal.

Here we describe TOMOMAN (TOMOgram MANager), an extensible open-sourced software package for handling cryo-electron tomography data preprocessing. TOMOMAN streamlines interoperability between a wide range of external packages and provides tools for project sharing and archival.

For the first time, a multimodal reconstruction of a magnetic thin-film structure has been found using polarised neutron reflectivity. This has been achieved by implementing the Bayesian approach in combination with error correction based on the maximum likelihood method and instrument function optimization.

This article reports an investigation into the effects of specific radiation damage to halogenated ligands in crystal structures of protein-inhibitor complexes.

We explain analysis of RIXS, HERFD and XR-HERFD data to discover new physical processes in manganese and manganese-containing materials, by applying our new technique XR-HERFD, developed from high resolution RIXS and HERFD.

The impact of sample thickness and experimental noise on angular correlation analysis from scanning electron nanobeam diffraction patterns of disordered carbon are investigated and analyzed regarding the interpretability of the analysis results.

The crystal structure of Cd5(TeO3)4(NO3)2 exhibits a distinct layered arrangement, whereas Cd4Te5O14 crystallizes with a framework structure.

In the complex, the ligand binds to the metal through an oxygen atom. The geometry of the seven-coordinate U atom is penta­gonal bipyramidal, with the uranyl O atoms in apical positions.

In the title compound, the tellurium(VI) and vanadium(V) atoms are statistically disordered over two of the ten metal-atom sites in the unprotonated [TeV9O28]5– heteropolyanion.

A chiral nickel(II) Schiff base complex derived from 2-hy­droxy­benzo­phenone and (1S,2S)-1,2-di­phenyl­ethyl­enedi­amine shows a λ conformation of the central di­amine chelate ring. The substituents on the C&z-dbnd;N carbon atoms significantly affect the circular dichroism spectra.

The crystal structure of a metabolite of the insecticide/acaricide etoxazole, designated R13 is presented along with a Hirshfeld surface analysis of inter­molecular inter­actions present in the crystal structure.

Theoretical and experimental structural studies of the title compound were undertaken using X-ray and DFT methods. The inter­actions present in the crystal were analyzed using Hirshfeld surface and MEP surface analysis. Docking studies with a covid-19 main protease (PDB ID: 6LU7) as the target receptor indicate that the synthesized compound may be a potential candidate for pharmaceutical applications.

The crystal structure of the co-crystal salt solvate 1,10-phenanthrolinium violurate violuric acid penta­hydrate features a tri-periodic hydrogen-bonded network with the violurate and violuric acid residues each assembled into tapes and the phenanthrolinium cations residing in channels.