Diffuse scattering in electron diffraction data from protein crystals

Diffuse background present in electron diffraction patterns from protein crystals can produce significant systematic error in intensity measurements. In certain regions of the diffraction pattern, this can even result in systematically negative intensity measurements. Thus, it is important to remove the diffuse background to produce more accurate measurement of structure factor amplitudes. The variable part of the continuous background arises from disorder in the crystal with an intensity which depends on the type of disorder. We show how the diffuse scattering can be calculated from a model for the disorder leading to a correction of intensities measured from diffraction patterns. For crystalline bacteriorhodopsin (bR) in native p3 (a = 62.45 Å) purple membrane the best correction for several models tested is obtained by assuming that the disorder comes from random displacement of the trimer of bR molecules as a rigid unit. The correction was applied to intensity measurements using improved error estimates based on the experimental errors. The number of intensities previously measured wrongly to be negative is about 10%. This is reduced by 4-fold to be in agreement with that expected from counting statistics. The final corrected amplitudes gave a lower R-factor when used for refinement of an atomic model.