Use of molecular replacement in the solution of an immunoglobulin Fab fragment structure

Molecular-replacement efficiency depends highly on structural and sequence homologies between available models and the molecule in the crystal being studied. The structure of the Fab fragment of an antibody specific for an influenza virus hemagglutinin was determined by molecular replacement and the Fv and the CH1:CL parts were localized separately. When rotation functions were calculated using known Fv structures as probes, a solution could not be found; this turns out to be due to an insufficient structural homology between the structure and the probes. When the structural homology between the Fv part and its model was enhanced by combining known structures of Fv domains based on sequence information, the right orientation was determined and confirmed by translation-function results. In the cases described here, a high contrast of the translation function was the most reliable criterion to detect a molecular-replacement solution.