Refinement of Protein and Nucleic Acid Structures

Refinement constitutes the last of the three main steps in the crystallographic establishment of a molecular structure, which are fast, crystal growth and data collection; second, phase determination and calculation of electron density maps; and third, model building and refinement. This final part is necessary because the structural models arrived at after the first two steps are approximate and usually contain errors in the tracing of the macromolecular chain. During the crystallographic refinement process, the macromolecular model is changed so that the agreement between the measured diffraction intensities and those calculated improves. This improved agreement between observed and calculated structure factors leads to better phases and, concomitantly, to improved electron density maps. The refinement process is monitored by the conventional crystallographic R factor, defined by the equation: