February 2022 issue
Utilities for atomic model validation in the CCP-EM software suite are discussed. An assessment of SARS-CoV-2 structures reflects a strong bias in model refinement towards geometric restraints when compared with agreement with the data.
Urate oxidase structures under high hydrostatic pressure per se and high argon pressure have been analyzed, deciphering the basis of protein–ligand stabilization by pressure and the formation of a transient intermediate dimeric substate during pressure-induced dissociation.
An end-to-end supervised learning method to directly recover missing orientations from 2D cryo-EM images is described.
A program utilizing artificial learning and convolutional neural networks, named Helcaraxe, has been developed which can detect ice-crystal artefacts in processed macromolecular diffraction data with unprecedented accuracy.
The direct observation of crystal defects in protein crystals induced solely by X-ray irradiation is reported.
In a pilot study, K-edge anomalous SAXS signal was obtained from a small dimeric protein containing polyhistidine tags bound to cupric ions, which can be used for the assessment of protein structural models in solution.
The first structure of a novel archaeal-like Holliday junction-resolving enzyme originating from a thermophilic phage was determined and its function in cleaving X-shaped dsDNA was demonstrated. Furthermore, a novel signature motif for Holliday junction-resolving enzymes originating from thermophilic bacteriophages is proposed.
The structure of an endo-β-1,4-glucanase from the cellulose-producing bacterium Enterobacter sp. CJF-002 bound to cellooligosaccharide was determined.
Using spatially resolved anomalous dispersion (SpReAD) refinement, the oxidation states of elements in crystal structures can be determined.
The crystal structure of guanosine monophosphate synthase from Aspergillus fumigatus, an attractive antifungal drug target, reveals unique differences from the human homologue that can be effectively targeted.
The streamlined crystallographic software tools for solving macromolecular crystal structures should be complemented with the visual aids that were used in the past (for example precession images and stereographic projections) to facilitate better understanding of the basic crystallographic concepts by younger aspiring crystallographers.