The structure of Chlamydomonas LOV1 as revealed by time-resolved serial synchrotron crystallography

The photo-reaction of the LOV1 domain of the Chlamydomonas reinhardtii phototropin is investigated by room-temperature time-resolved serial crystallography. A covalent adduct forms between the C4a atom of the central flavin-mononucleotide chromophore and a protein cysteine. The structure of the adduct is very similar to that of LOV2 determined 23 years ago from the maidenhair fern Phy3.

AI-enhanced X-ray diffraction analysis: towards real-time mineral phase identification and qu­antification

The use of convolutional neural networks can revolutionize XRD analysis by significantly reducing processing times. Demonstration against synthetic and real mineral mixture data provide a first assessment of the accuracy of such methods.

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

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.

Many locks to one key: N-acetyl­neuraminic acid binding to proteins

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.

Structural characterization of TIR-domain signalosomes through a combination of structural biology approaches

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.

Crossing length scales: X-ray approaches to studying the structure of biological materials

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.

Structure of Aquifex aeolicus lumazine synthase by cryo-electron microscopy to 1.42 Å resolution

A near-atomic resolution map was obtained for lumazine synthase while benchmarking a new microscope. At this resolution, waters, ligands and hydrogens were visible. A detailed outline of the methods used is presented that can employed for any single-particle cryo-EM experiment.

Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data

Kinematical Hirshfeld atom refinement has been applied to electron diffraction data for the first time, but the effect of using an aspherical atom model is overshadowed by dynamical scattering effects. Dynamical independent atom model refinement leads to significantly improved structures, suggesting that dynamical refinement is also necessary to obtain the full advantage of using aspherical atom models.

Structure–property relationship of a complex photoluminescent arylacetylide-gold(I) compound. I: a pressure-induced phase transformation caught in the act

A pressure-induced triclinic-to-monoclinic phase transition has been caught `in the act' in the course of a wider series of high-pressure synchrotron diffraction experiments conducted on a moderately photoluminescent gold(I) compound. Our experiments illustrate how conducting a fast series of experiments, enabled by modern equipment at synchrotrons, can lead to an inaccurate estimation of the actual pressure of a phase transformation.

From formulation to structure: 3D electron diffraction for the structure solution of a new indomethacin polymorph from an amorphous solid dispersion

3D electron diffraction (3DED) was used to elucidate the structure of a new ninth polymorph of indomethacin from an amorphous solid dispersion, which are product formulations used to improve the dissolution performance of active pharmaceutical ingredients with poor aqueous solubility. Insights from the structure solution allowed for a simpler crystallization route for this polymorph to be deduced, demonstrating the relevance of 3DED within drug development.

Fixed-target pump–probe SFX: eliminating the scourge of light contamination

Time-resolved serial femtosecond crystallography experiments can be performed with samples delivered on solid supports. Sample consumption is significantly reduced when compared with the popular crystal-delivery system via high-viscosity extrusion.

Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data

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.

In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry

The determination of a challenging structure in the P1 space group, the lowest symmetry possible, shows how our in situ serial crystallography approach expands the application of crystallization plates as a robust sample delivery method.

Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography

A crystalline sample of CrLOV1 was optimized for serial crystallography. Time-resolved serial synchrotron crystallography provides high-resolution insights into structural changes of CrLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, resolving the geometry of the thio­ether adduct and alteration of the C-terminal region implicated in the signal transduction.

Texture tomography, a versatile framework to study crystalline texture in 3D

The crystallographic texture is a key feature of crystalline organization in materials, yet no technique exists to locally characterize complex textured materials in 3D. In this manuscript, we present Texture Tomography (TexTOM) as a computational tool to provide full 3D texture information from X-ray diffraction measurements.

Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser

State-of-the-art 3D cryo-EM map denoising with a self-supervised neural network model optimized for theoretical noise-free maps is introduced.

Exploring serial crystallography for drug discovery

In this work, serial crystallography is applied to a drug discovery target and the room-temperature ligand-bound complexes are used to explore temperature-dependent structural differences.

The crystal structure of olanzapine form III

This paper reports the crystal structure determination of olanzapine form III by 3D electron diffraction, the last unknown anhydrous polymorph in the olanzapine complex polytypism scenario.

Binding structures of SERF1a with NT17-polyQ peptides of huntingtin exon 1 revealed by SEC-SWAXS, NMR and molecular simulation

Binding structures of SERF1a with the N-terminal fragment of huntingtin exon 1 and NT17-polyQ peptides are revealed using an integrated analysis of size-exclusion-column-based small- and wide-angle X-ray scattering (SEC-SWAXS), NMR, and molecular simulation.

Phase qu­antification using deep neural network processing of XRD patterns

A deep neural network approach to the identification and quantification of powder X-ray diffraction patterns was applied and proved successful for the quantitative description of complex mineralogical assemblages consisting of up to four minerals with different structures, including different space groups, for which data augmentation is not straightforward.

CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data

Recent updates to CheckMyMetal have significantly enhanced its capability to efficiently handle large datasets, including those generated from cryo-EM structural analyses.

On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors

We apply for the first time the transferable aspherical atom model (TAAM) for the refinement of a metal complex structure against 3D ED data. Our results show that TAAM significantly outperforms the independent atom model (IAM) by more accurately depicting the electrostatic potential, particularly in low-resolution ranges. We found that using TAAM for organic ligands is more important than an accurate description of the metal centre in the refinement against 3D ED data.

A predicted model-aided one-step classification–multireconstruction algorithm for X-ray free-electron laser single-particle imaging

A predicted model-aided one-step classification–multireconstruction algorithm for X-ray free-electron laser single-particle imaging is proposed. The algorithm is capable of processing mixed diffraction patterns from multiple molecules, classifying diffraction patterns by different molecules, determining their orientations and reconstructing multiple 3D diffraction intensities, in one step.