Nobuhiro Go

Refinement of X-ray data on proteins. I. Adjustment of atomic coordinates to conform to a specified geometry☆

The atomic coordinates of a protein derived from x-ray-diffraction studies yield bond lengths and bond angles which depart significantly from those obtained from the crystal structures of the individual amino acids. A method is described for adjusting the dihedral angles (φi , ψi , χj) of the backbone and side chains by a least-squares approximation to the x-ray coordinates so that the computed structure conforms to those derived from crystal structures of its constituent amino acids. This structure may then be used as a starting point for conformational energy calculations. The performance of various minimization procedures in the least-squares computations is described, and a comparison of the adjusted structure with the x-ray structure is made in terms of deviations of the atom positions and dihedral angles from their original values. The method is applied here to the x-ray coordinates of lysozyme and chymotrypsin.