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Estimation of uncertainties in X‐ray refinement results by use of perturbed structures
Author(s) -
Kuriyan John,
Karplus Martin,
Petsko Gregory A.
Publication year - 1987
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340020102
Subject(s) - minification , isotropy , energy minimization , myoglobin , x ray , harmonic , energy (signal processing) , physics , crystallography , computational physics , chemistry , mathematics , mathematical optimization , quantum mechanics , organic chemistry
The uncertainties in the refined parameters for a 1.5‐Å X‐ray structure of carbon‐monoxy (FeII) myoglobin are estimated by combining energy minimization with least‐squares refinement against the X‐ray data. The energy minimization, done without reference to the X‐ray data, provide perturbed structures which are used to restart conventional X‐ray refinement. The resulting refined structures have the same, or better, R‐factor and stereochemical parameters as the original X‐ray structure, but deviate from it by 0.13 Å rms for the backbone atoms and 0.31 Å rms for the sidechain atoms. Atoms interacting with a disordered sidechain, Arg 45 CD3, are observed to have larger positional uncertainties. The uncertainty in the B‐factors, within the isotropic harmonic motion approximation, is estimated to be 15%. The resulting X‐ray structures are more consistent with the energy parameters used in simulations.