Section 19.2.4.4. Refinement

In order to arrive at a correct mechanistic model for the protein, an accurate atomic structure is needed. So far, in electron crystallography only bacteriorhodopsin has been refined (Grigorieff et al., 1996). A common criterion used in X-ray crystallography to evaluate the progress of refinement is based on the free R factor, which measures the agreement between the model and a part of the experimental data not included in the refinement process. In electron crystallography, the phases are measured independently from images and hence are not refined. Therefore, they can be used as a `free phase residual,' which is analogous to the free R factor, to assess the progress of refinement. The refined structure would result in improved peptide geometry, increased accuracy of the coordinates of the polypeptide backbone and of the amino-acid side chain residues, and improved temperature factors of the residues.