Optimization of the energy constant of the methionine S^δ—C^[epsilon] bond for X-PLOR refinement of protein structure

The bond energy constant of methionine S^δ—C^[epsilon], 170.066 kcal mol⁻¹ Å⁻², is given as a default value in X-ray protein structure refinement with X-PLOR [Brünger (1992). X-PLOR Version 3.1. A system for X-ray Crystallography and NMR. New York University Press]. When the atomic parameters of 3564 amino acid residues of bovine heart cytochrome c oxidase were refined at 2.0 Å resolution by using X-PLOR with default restraining parameters, 36 bond lengths deviated by over 0.06 Å from their ideal values. Out of the 36 bonds, 25 were methionine S^δ—C^[epsilon] bonds. Refinement with an energy parameter of 500.0 kcal mol⁻¹ Å⁻² for the methionine S^δ—C^[epsilon] bond resulted in convergence of the S^δ—C^[epsilon] bond lengths to within 0.06 Å from their ideal values and reduced the crystallographic R and free-R factors by 0.6 and 0.3%, respectively. Consequently, a strong bond energy constant for S^δ—C^[epsilon] of 500.0 kcal mol⁻¹ Å⁻² is recommended instead of the default value of 170.066 kcal mol⁻¹ Å⁻².