Estimation of uncertainties in X-ray refinement results by use of perturbed structures

✍ Scribed by Dr. John Kuriyan; Dr. Martin Karplus; Gregory A. Petsko

• Publisher: John Wiley and Sons
• Year: 1987
• Tongue: English
• Weight: 901 KB
• Volume: 2
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/prot.340020102

✦ Synopsis

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.