Electron-density Maps and Refinement of Protein Structures

InterpretatioD of Electron-density Maps and Refinement of Protein Structures.—Now that so many proteins have been determined at high resolution, improving the fit of the protein model to the electron density and improving the electron density itself have become central problems. 

Barry and North describe a computer-controlled display system in which the electron-density map is conveniently represented by computing single contours in three orthogonal directions and displaying the appropriate projections. The peptide conformations and the electron dmisity are displayed on a cathode ray tube, and the illusion of three dimensions may be obtained by viewing a stereoscopic pair of projections, or by displaying 

The difference Fourier technique is also very useful in refinement of protein structures. An analysis of the errors and their treatment is discussed by Henderson and Moffat, who find that a difference Fourier map is able to detect much smaller features of electron density than those revealed by a normal Fourier map with the same phases. 

Jensen et al. have very successfully used difference Fourier maps using phases calculated from the atomic co-ordinates, in the refinement of the structure of the small protein, rubredoxin. Shifts derived from the first difference Fourier synthesis at 1.5 A resolution reduced the R factor (the agreement factor) from 0.372 to 0.321. Eventually difference syntheses revealed the positions of 127 water molecules oxygen atoms representing water were included if peaks were present in the 2 A isomorphous phased Fourier as well as the difference Fourier map. Occupancy factors were made proportional to peak height. This led to an appreciable decrease in R. After calculation of four difference Fourier syntheses, the method of least squares was used to refine the positional and thermal parameters despite the fact that their number was exceeded by the number of structure factors by 

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