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Optimization of the energy constant of the methionine S δ —C ɛ bond for X‐PLOR refinement of protein structure
Author(s) -
Odoko Mamiko,
Yao Min,
Yamashita Eiki,
Nakashima Ryosuke,
Hirata Kunio,
Aoyama Hiroshi,
Muramoto Kazumasa,
ShinzawaItoh Kyoko,
Yoshikawa Shinya,
Tsukihara Tomitake
Publication year - 2001
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889800019944
Subject(s) - bond length , chemistry , crystallography , bond energy , molecular geometry , methionine , molecule , crystal structure , amino acid , organic chemistry , biochemistry
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 .