Direct structure analysis in protein electron crystallography via the density histogram: deoxycholate-treated purple membrane

Abstract

The crystal structure of bacteriorhodopsin in purple membrane treated with sodium deoxycholate (plane group p3, a = 57.3 Å) was solved ab initio in projection from previously published electron diffraction amplitudes to 6.2 Å by direct methods for crystallographic phase determination. The best solution form the Sayre equation was identified by minimizing the skew properties of the cross-correlation of the experimental density histogram with the expected histogram. After Fourier refinement, the overall mean phase error is 43.3° for all 35 unique reflections of 16.9° for the 14 most intense maxima. For six clearly identified helix sites, the mean deviation of positions, when compared to the original model, was 0.7 Å.