SASBDB reaches 5000 data sets: empowering open science and next-generation SAS analysis

The Small-Angle Scattering Biological Data Bank (SASBDB) has surpassed 5000 deposited data sets, highlighting its role as a central open-access resource for biological small-angle scattering data and its growing impact on method development, benchmarking and data-driven analysis.

CryoJAX: a cryo-electron microscopy image-simulation library in JAX

The authors have developed cryoJAX, a cryo-EM image-simulation library for developing data-analysis techniques across cryo-EM modalities. CryoJAX is built on JAX, an emerging scientific computing framework in Python well suited for cryo-EM data analysis.

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements

Cryo-ET is a rapidly emerging technique that enables 3D visualization of complex biological structures, but present limits on signal-to-noise ratio and reconstruction quality pose challenges for downstream analysis. Here, we present a systematic analysis of state-of-the-art deep-learning methods for contrast enhancement and propose improvements in neural network architectures and training objectives to preserve more high-resolution information.

Coupled on-line in crystallo UV–Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins at room versus cryogenic temperature

We used on-line in crystallo UV–Vis absorption spectroscopy in conjunction with X-ray crystallography on beamline BM07-FIP2 at the ESRF to compare the structural effects of specific radiation damage on two different metal-containing proteins at either room or cryogenic temperature.

X-ray beam effects on metallo-peptides reflect redox events: insights from X-ray absorption spectroscopy measurements on metal complexes of truncated amyloid-β peptides

X-ray exposure influences the structures of Cu(I), Cu(II) and Zn(II) complexes of amyloid-β (Aβ) peptides in different ways. While Cu(I) and Zn(II) complexes show no detectable X-ray-induced spectral changes, Cu(II) complexes undergo significant spectral evolution under irradiation. Experiments on the truncated fragments Aβ_1–6 and Aβ_1–16 show that the extent of relaxation depends on the peptide length, on the binding mode and on the temperature.

Radiation-dose effects in correlative X-ray/cryo-electron microscopy of frozen-hydrated biological samples

Cryo-EM analysis of apoferritin exposed to an X-ray dose of 100 MGy confirms the potential for high-resolution correlative imaging workflows combining X-ray tomography and cryo-EM.

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

A database of validated ligand restraints computed using various levels of quantum mechanics is generated and distributed with Phenix to streamline and improve macromolecular refinement results.

Decision-making in serial crystallography: a simple test to quickly determine whether sufficient data have been collected

We describe a simple test to determine whether sufficient data have been collected during a serial crystallographic experiment, and its incorporation into the autoprocessing pipeline at the T-REXX endstation on beamline P14 at the PETRA III synchrotron.

Updating direct methods V. Phasing when triplet invariants are estimated via the Patterson map

Crystal structures of proteins and nucleic acids with data resolution up to 2.2 Å are solved via a novel direct-methods program using the Pattterson map as prior information.

Phosphatidylinositol transfer protein α binds microcolins in its open conformation

We report the crystal structure of human PITPα in complex with microcolin H at 2.0 Å resolution, revealing that microcolins bind covalently within the lipid-binding cavity and stabilize PITPα in an open conformation with a markedly enlarged cavity relative to the lipid-bound state. These results define the structural basis of PITP inhibition by microcolins and underscore the importance of using ligand-bound conformations for accurate structure-based modeling.

Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies

This article describes the transition of the Glass laboratory from X-ray crystallography to single-particle cryo-electron microscopy (cryo-EM) for structural studies of ATAD2B, a large AAA+ ATPase- and bromodomain-containing protein involved in chromatin regulation. It outlines practical strategies for protein expression, sample preparation, data processing and model building, offering a comprehensive workflow and troubleshooting guide for new cryo-EM users working with large, flexible macromolecular complexes.