Patterson correlation refinement

Phase information was obtained by combining an X-ray structure of the major capsid protein with a cryo-EM reconstruction of the virus. The position and orientation of this model were refined against the experimental data, separately for the two crystal forms, using XPLOR3.1 (Brunger, 1992). An initial estimate of the particle orientation was obtained from a self-rotation fimction. Patterson correlation refinement was performed against 60-15 A resolution data to optimize the orientation. The position and orientation of the particle were then... 

Patterson Correlation Refinement. To select which of the orientations determined from the rotation search is the correct solution a Patterson correlation refinement of the peak list of the rotation function was performed. This was carried out by minimization against a target function defined by Brunger (1990) and as implemented in XPLOR. The search model, P2, was optimized for each of the selected peaks of the rotation function. 

Figure 8.4 Rotation function results P2 into crystalline ALBP. (a)Plot of the 101 best solutions to the rotation function, each peak numbered in the horizontal direction (abscissa). The correlation between the Patterson s of the probe molecule and the measured ALBP X-ray results are shown in the vertical direction (ordinate) and are given in arbitrary units. (b) Description of the rotation studies after Patterson correlation refinement. The peak numbers plotted in both panels (a)and (b) are the same. Reprinted with permission from Z. Xu et al. (1992) Biochemistry 31,3484-3492. Copyright 1992 American Chemical Society.

Each refined orientation of the probe received a correlation coefficient that shows how well it fits the Patterson map of ALBP. The orientation receiving the highest correlation coefficient was taken as the best orientation of the probe, and then used to refine the position of the probe in the ALBP unit cell. The orientation and position of the model obtained from the molecular replacement search was so good that refinement of the model as a rigid body produced only slight improvement in R. The authors attribute this to the effectiveness of the Patterson correlation refinement of model orientation, stage two of the search. 

Brunger, A. T. (1990). Extension of molecular replacement a new search strategy based on Patterson correlation refinement., Acta Crystallogr, A46, 546-593. 

Translation Search. A translation search was done by using the P2 probe molecule oriented by the rotation function studies and refined by the Patterson correlation method. The translation search employed the standard linear correlation coefficient between the normalized observed structure factors and the normalized calculated structure factors (Funinaga Read, 1987 Brunger, 1990). X-ray diffraction data from 10-3 A resolution were used. Search was made in the range x = 0-0.5, y = 0—0.5, and z = 0-0.5, with the sampling interval 0.0125 of the unit cell length. 

As discussed later in the "Results" section, the rotation function contains many peaks. The strongest 100 peaks are selected, and each orientation is refined by least squares to produce the best fit to the ALBP Patterson map. For each refined orientation, a correlation coefficient is computed. The orientation giving the highest correlation coefficient is chosen as the best orientation for the phasing model. 

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