Application of the molecular replacement method to multidomain proteins. 2. Comparison of various methods for positioning an oriented fragment in the unit cell.

The capabilities of several different methods to determine the correct translation of a model for the application of the molecular replacement method of structure determination to multidomain proteins have been analyzed. The structure of the Fab fragment of the autoimmune anti-poly(dT)-specific antibody HED10 was determined using molecular replacement and provides an example for comparing different methods of determining the correct translation of the model and for evaluating the importance of the parameters used. Expansion to space group P1 and phasing with a correctly oriented randomly positioned model was found to be superior to either the Crowther-Blow translation function [Crowther & Blow (1967). Acta Cryst. 23, 544-548] or a brute-force search when only a small part of the molecule was used as a model.