Synchrotron radiation in atomic-resolution studies of protein structure

Abstract

The paper discusses the high resolution and quality aspects of synchrotron radiation protein crystallography using examples from our own laboratory. The examples include two inhibitors of trypsin, one (CMTI) derived from plants, and one (BPTI) of mammalian origin. The structures were refined at 1 Å (CMTI) and 0.86 Å (BPTI) resolution to final R-factors of 0.114 and 0.103, respectively. In both cases it was possible to use anisotropic displacement parameters and to relax or remove some of the stereochemical restraints that are necessary in lower-resolution refinements. The results indicate that some of the standards are not exactly correct. For instance, the peptide group shows large deviations from planarity, and the N–Cα–C angle has a wide spread. Compared to lower-resolution refinements, more residues are modeled in alternative conformations. From the final full-matrix least-squares refinements, the estimated standard errors in bond lengths are about 0.005–0.01 Å (BPTI) and 0.01–0.03 Å (CMTI). These numbers demonstrate the tremendous improvement in quality when resolution is extended from 1.0 to 0.86 Å. In line with this is the presence of clear difference electron density peaks corresponding to H atoms, including those in water molecules, in the BPTI structure, but not in the CMTI structure. Some of them are seen to form C–H…O and N–H…π H bonds.