Abstract
Crystallographic structure models in the Protein Data Bank (PDB) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures, especially at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. Using approximately 60 years of CPU-time in massively parallel computing, we constructed a new instance of the PDB-REDO databank, a novel resource to help biologists gain insight on protein families or on specific structures, as we demonstrate with examples.
Footnotes
↵# Shared first authors