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