Journal of Applied Crystallography

Volume 34, Part 1 (February 2001)

short communications

J. Appl. Cryst. (2001). 34, 80-81 [ doi:10.1107/S0021889800019944 ]

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

M. Odoko, M. Yao, E. Yamashita, R. Nakashima, K. Hirata, H. Aoyama, K. Muramoto, K. Shinzawa-Itoh, S. Yoshikawa and T. Tsukihara

Abstract: The bond energy constant of methionine S-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 S-C bonds. Refinement with an energy parameter of 500.0 kcal mol^-1 Å^-2 for the methionine S-C bond resulted in convergence of the S-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 S-C of 500.0 kcal mol^-1 Å^-2 is recommended instead of the default value of 170.066 kcal mol^-1 Å^-2.

Keywords: proteins; macromolecules; bond energy constant; structure refinement.