October 2020 issue
Macromolecular atomic B-value distributions have been modelled using a mixture of shifted inverse-gamma distributions. B-value and resolution-dependent local ADP differences have also been applied for the validation of heavy atoms and ligands.
A crystal-mounting platform has been developed for native SAD phasing. This platform includes a newly designed solution-free tool and an automatic freezing–extracting robot for use at synchrotron facilities.
Large crystals for neutron diffraction experiments were cooled anaerobically by two methods, cooling in a cold gas stream and plunge-cooling into liquid nitrogen, and their respective effects on crystal quality were compared. Gas-stream cooling was sufficient to suppress the increase in mosaicity over the entire crystal, leading to success in the first data collection for a membrane-bound hydrogenase from Desulfovibrio vulgaris in its active reduced form.
TRIM-protein RING domains commonly exist in a weak monomer–dimer association; here, it is shown that the RING domain of TRIM69 forms a tight dimer and the structure is used to discuss the reasons for this high-affinity interaction.
Helical ensembles solve more structures by MR with AMPLE than do ideal helices and at no greater CPU cost.
Four very efficient scavengers for BioSAXS experiments, three nucleosides and one nitrogenous base, are described. The critical radiation doses of the tested protein solutions increase by up to 20 times when adding these compounds, without altering the stability of the protein or reducing the contrast, allowing BioSAXS experiments on low-molecular-weight and low-concentration protein samples.
Biochemical studies and crystal structures of complexes of M. smegmatis MutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP led to the elucidation of a relationship between intermolecular interactions, molecular plasticity and the action of the enzyme on nucleotides, in addition to providing insights into the modulation of specificity by the ligand conformation.
Vasohibin-1 and small vasohibin-binding protein (SVBP) form an intermolecular heterotetramer in the crystal. The heterotetramer was stabilized by exchange of the conserved N-terminal region.
Data from multiple solvent-soaked crystal structures were used to improve model quality, to identify bound organic molecules at sites involved in protein–protein interactions and to identify a conserved water network that governs DNA binding. A differential B-factor analysis identifies the regiospecific effects of various solvents on protein mobility.
The crystal structure of CYRI-B is revealed, providing a template to understand the role of this highly conserved eukaryotic protein in a variety of actin-dependent cellular processes.
Orienting the deuterium atoms of water molecules in neutron crystal structures can be tedious task for the crystallographer. An automated method is presented to systematically reorient water molecules and decide which are correctly oriented.
The chemokine CXCL13 relies on its N-terminus for signaling, but minor length and side-chain variations still result in a agonistic forms of the protein. Two crystal structures reveal that both the N-terminus and the C-terminal extension of the protein are highly flexible, whereas the core domain of the protein is rigid.