Estimation of uncertainties in X-ray refinement results by use of perturbed structures.
The uncertainties in the refined parameters for a 1.5-A 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 minimizations, 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 A rms for the backbone atoms and 0.31 A 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.
Kuriyan
J
J
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Karplus
M
M
Petsko
G A
GA
D001120:Arginine; D001665:Binding Sites; D008956:Models, Chemical; D009211:Myoglobin; D011487:Protein Conformation; D013816:Thermodynamics; D014961:X-Ray Diffraction
D009211:Myoglobin; C018013:carboxymyoglobin; D001120:Arginine