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Generalized Molecular Replacement

The following sections show how the 26-10 Fab fragment complexed with digoxin was solved by generalized molecular replacement (Brünger, 1991c). The space group of the 26-10 Fab/digoxin crystals is

(Strong, 1990), with the b-axis unique, and a non-crystallographic twofold symmetry is present. The following strategy was employed to solve the structure:

Self-rotation function.
Modification of the elbow angle of a known Fab structure.
Cross-rotation function with the modified Fab structure.
Filtering the rotation function by -refinement.
Analysis of the -refinement.
Translation function for molecule A, using the -refined model.
Translation function for molecule B.
Combined translation function to determine the relative position between A,B.
Rigid-body refinement.

In general, one has to try several different starting elbow angles (spaced approximately 10 $^{\circ}$ apart) and repeat steps 3-6 until a good solution is found. This strategy is also applicable to other multidomain proteins or PC-refinements of other degrees of freedom. The modification of the Fab example input files should be straightforward. An overview of the strategy is shown in Fig. 19.1.

**Figure 19.1:** Overview of molecular replacement.
$\begin{figure}{\epsfxsize =320pt \noindent\epsffile{pc.eps} }\end{figure}$

Subsections

Xplor-NIH 2025-03-21