Neutron crystallographic refinement with REFMAC5 from the CCP4 suite

The macromolecular refinement package REFMAC5 from the CCP4 suite has been extended by the incorporation of algorithms for neutron crystallography.

The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions

The explicit refinement of Ramachandran, rotamer and clash criteria at now-prevalent lower resolutions (2.5–4 Å) has made the current, traditional model validation at the Protein Data Bank nearly useless in this range, since quite poor structures can have perfect scores. Fortunately, new criteria and programs such as ISOLDE, CaBLAM and AlphaFold are coming to the rescue, are already very useful and should be extensible into an effective new community standard.

Improved joint X-ray and neutron refinement procedure in Phenix

The improved joint X-ray and neutron refinement procedure in Phenix optimizes two different models against the X-ray and neutron data sets. This approach is shown to reduce overfitting compared with refining the models separately.

Structural mechanism of Escherichia coli cyanase

The crystal structures of different states of cyanase, i.e. native, cyanate-bound, bicarbonate-bound and reaction states, obtained using synchrotron X-rays and X-ray free-electron lasers, elucidate the reaction intermediates and molecular dynamics of the active site.

Using graphlet degree vectors to predict atomic displacement parameters in protein structures

The components of the graphlet degree vector, which describes the complexity of the wiring of a given atom, can be used in a multiple linear regression model to predict atomic displacement parameters in protein structures.