Bulk-solvent correction in large macromolecular structures.
The estimation of the bulk-solvent contribution to the diffraction of a macromolecular crystal makes use of a solvent mask which delimits the bulk-solvent regions in the crystal. It is shown that the way this mask is usually defined in CNS contains a bias which can lead to absurd results in the case of very large structures, where the calculations can only be made on relatively coarse grids. A modified procedure is described and applied to 70S ribosome data at 5.5 A resolution. The B factor affecting the bulk solvent is also discussed. Even in this case of very high and widely variable atomic B factors, it seems sufficient to consider a constant and isotropic B factor for the bulk solvent. This is initially set to the average value of the atomic B factor, but can be refined.
Rees
Bernard
B
Laboratoire de Biologie et Génomique Structurales, IGBMC, 1 Rue Laurent Fries, BP 10142, 67400 Illkirch Cedex, France. rees@igbmc.u-strasbg.fr
Jenner
Lasse
L
Yusupov
Marat
M
D046911:Macromolecular Substances / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry; D012997:Solvents / Q000737:chemistry*; D016963:Thermus thermophilus; D014961:X-Ray Diffraction / Q000379:methods*
D046911:Macromolecular Substances; D012997:Solvents