Ten years of the CCP-EM Spring Symposium

This article reviews the growth over the last ten years of the CCP-EM Spring Symposium. The conference is now established as a popular meeting for practitioners of life-science cryoEM and highlights new methods and exemplar applications.

CryoLike: a Python package for cryo-electron microscopy image-to-structure likelihood calculations

We present CryoLike, a user-friendly Python workflow for calculating the image-to-structure likelihood in cryo-electron microscopy.

Completion of partial structures using Patterson maps with the CrysFormer machine-learning model

We integrate existing machine learning-based protein structure-prediction methods with X-ray crystallography by completing partial structures derived from AlphaFold predictions and the corresponding Patterson map information. The CrysFormer results are promising when applied to an initial data set of 15-residue fragments in P2₁ unit cells.

Xtricorder: a likelihood-enhanced self-rotation function and application to a machine learning-enhanced Matthews prediction of asymmetric unit copy number

Xtricorder is a tool for analysing crystallographic data, featuring a likelihood-enhanced self-rotation function and a novel `composite-section diagram' thereof, which aids interpretation and enables a machine learning-enhanced prediction of asymmetric unit content.

Limiting the effects of radiation damage in MicroED through dose selection during data processing

The effect of radiation damage in MicroED has been studied. By only including data collected at low accumulated electron dose during data processing, the effects of radiation damage can be reduced.

A structural basis for the strain-dependent UDP-sugar specificity of glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system

X-ray crystal structures of glycosyltransferase C from the Limosilactobacillus reuteri 100-23 (LrGtfC_100-23) accessory secretion system were determined in its apo form and in complexes with UDP and with UDP-N-acetylglucosamine, which revealed candidate residues involved in strain-specific recognition of UDP-sugars. Site-directed mutagenesis of these residues led to a switch of the UDP-sugar binding specificities of LrGtfC_100-23 and the highly homologous LrGtfC from L. reuteri ATCC 53608.

Polo-like kinase 1–inhibitor co-complex structures via the surface-entropy reduction approach and a DARPin-assisted approach

A surface-entropy reduction approach for human Polo-like kinase 1 (PLK1) enabled a reproducible and robust crystallization system for this cancer drug target. Co-crystal structures with representatives of three different small-molecule inhibitor classes were elucidated. For two of them, co-crystal structures with PLK1 were also determined via a previously published crystallization approach using a designed ankyrin-repeat protein (DARPin), and the two approaches are compared.

Exploration of questionable backbone conformations in crystallographic structure models using a structural alphabet

We present a protocol to detect and characterize questionable backbone conformations in X-ray protein structure models. These conformations may arise from artifacts related to the crystallization process or from errors introduced during model building and refinement. Applied to 826 proteins and illustrated by a case study on HIV-2 protease, the analysis revealed that nearly one fifth of residues are affected and that these conformations may influence the fold of certain regions and raise questions about their biological relevance.

Hydrogen density mapping in biomolecular crystals through dynamic nuclear polarization

Dynamic nuclear polarization enables spin-contrast variation to open up new possibilities in amplifying the hydrogen signal from neutron crystallography. We analyze the phase ambiguity and devise a computational method to reconstruct the hydrogen density.