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The x-ray structure of rubredoxin has been refined by energy minimization. The computed structure is constrained to have standard bond lengths, bond angles, and planar trans peptide groups. Also, since most of the steric overlaps have been relieved, it has a very low energy. As judged by the root mean square (RMS) deviation of the computed coordinates from those of the x-ray structure, the two are very similar. The reliability index R for the computed structure (determined from the structure factors for the calculated conformation) is 0.37, which is comparable to that for other proteins.

Refinement of the X-ray Structure of Rubredoxin by Conformational Energy Calculations