Biomedical subjects
Publications and source records attributed to Andrei Fokine.
The connectivity-based phasing method has been applied independently to three neutron diffraction data sets obtained from the same crystal of tRNA(Asp)-aspartyl-tRNA synthetase complex but at different concentrations of D(2)O/H(2)O, thus masking different components of the crystal. The obtained low-resolution images correlate perfectly with the solvent level.
A bulk-solvent correction is regularly used for macromolecular refinement. The flat model of the bulk solvent is considered to be the most reliable. It is shown that the standard procedure does not always result in the optimal values of the bulk-solvent correction parameters. A method to obtain the best values for parameters k(sol) and B(sol) of the flat-solvent model is discussed. The values of correctly determined parameters for crystallographic structures deposited in the Protein Data Bank are clustered around k(sol) = 0.35 e A(-3) and B(sol) = 46 A(2), which have a reasonable physical meaning. Such a distribution allows the use of these mean values of solvent parameters for many practical applications when refined parameters cannot be obtained, especially when an atomic model in the unit cell is not yet known.
Low-resolution reflections (approximately 15 A and lower) are very useful for the translation search in molecular replacement because they are less sensitive to model errors compared with the traditionally used reflections of resolution 4-10 A. At low resolution, however, the contribution from the bulk solvent is quite significant and corresponding structure factors calculated from a macromolecular model cannot be compared with experimental values if this contribution is neglected. The proposed method provides a way of fast translation searches where low-resolution reflections are taken into account. Test calculations using several experimental data sets show a dramatic improvement in the signal after the bulk-solvent correction and low-resolution reflections were included in the calculation; this improvement allowed unambiguous identification of the solution.