Optimization of the energy constant of the methionine S δ —C ɛ bond for X‐PLOR refinement of protein structure

The bond energy constant of methionine S δ —C ɛ , 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 ɛ bonds. Refinement with an energy parameter of 500.0 kcal mol −1  Å −2 for the methionine S δ —C ɛ bond resulted in convergence of the S δ —C ɛ 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 ɛ of 500.0 kcal mol −1  Å −2 is recommended instead of the default value of 170.066 kcal mol −1  Å −2 .