Optimization of the energy constant of the methionine (S delta-C epsilon) bond for X-PLOR refinement of protein structure

The bond energy constant of methionine S-delta-C-epsilon, 170.066 kcal mol( -1) Angstrom (-2), is given as a default value in X-ray protein structure r efinement with X-PLOR [Brunger (1992). X-PLOR Version 3.1. A system for X-r ay Crystallography and NMR. New York University Press]. When the atomic par ameters of 3564 amino acid residues of bovine heart cytochrome c oxidase we re refined at 2.0 Angstrom resolution by using X-PLOR with default restrain ing parameters, 36 bond lengths deviated by over 0.06 Angstrom from their i deal values. Out of the 36 bonds, 25 were methionine S-delta-C-epsilon bond s. Refinement with an energy parameter of 500.0 kcal mol(-1) Angstrom (-2) for the methionine S-delta-C-epsilon bond resulted in convergence of the S- delta-C-epsilon bond lengths to within 0.06 Angstrom from their ideal value s and reduced the crystallographic R and free-R factors by 0.6 and 0.3%, re spectively. Consequently, a strong bond energy constant for S-delta-C-epsil on of 500.0 kcal mol(-1) Angstrom (-2) is recommended instead of the defaul t value of 170.066 kcal mol(-1) Angstrom (-2).