Improved dihedral-angle restraints for protein structure refinement

Because of the relatively low-resolution diffraction of typical protein crystals, structure refinement is usually carried out employing stereochemical restraints to increase the effective number of observations. Well defined values for bond lengths and angles are available from small-molecule crystal structures. Such values do not exist for dihedral angles because of the concern that the strong crystal contacts in small-molecule crystal structures could distort the dihedral angles. This paper examines the dihedral-angle distributions in ultra-high-resolution protein structures (1.2 Å or better) as a means of analysing the population frequencies of dihedral angles in proteins and compares these with the stereochemical restraints currently used in one of the more widely used molecular-dynamics refinement packages, X-PLOR, and its successor, CNS. Discrepancies between the restraints used in these programs and what is actually seen in high-resolution protein structures are examined and an improved set of dihedral-angle restraint parameters are derived from these inspections.