REMARKS ABOUT PROTEIN STRUCTURE PRECISION
Durward Cruickshank
Chemistry Department, UMIST, Manchester M60
1QD, UK
dwj_cruickshank@email.msn.com
Full-matrix least-squares is advocated (1) as a good method for assessing protein structure precision in restrained refinements for both high and low resolution analyses.
High resolution 0.94 A data for the 237 residue protein concanavalin A were used (2) in unrestrained and restrained full-matrix inversions to provide e.s.d.'s s(r) for positions and s(l) for bond lengths. s(r) is as small as 0.01 A for atoms with low Debye B values but increases strongly with B. The unrestrained s(l) also increase strongly with B, but the restrained s(l) do not increase above the stereochemical-dictionary values. The results emphasise the distinction between unrestrained and restrained refinements and between s(r) and s(l). Complete full-matrix inversions, alas, require massive calculations.
Several approximate methods are examined and compared critically. These include a Fourier map formula (3,4), Luzzati plots (5), and a new Diffraction-component Precision Index (1). The DPI estimate of s(r,Bavg) is given by a simple formula. It uses R or Rfree and is based on a very rough approximation to the least-squares method. Many examples show its usefulness as a precision comparator for high and low resolution structures.
The effect of restraints as resolution varies is examined.
With the increasing power of computers, more regular use of
full-matrix inversion is urged to establish positional precision,
and hence the precision of non-dictionary distances, in both high
and low resolution structures. Failing this, parameter blocks for
representative residues and their neighbours should be inverted
to gain a general idea of s(r)
as a function of B. The whole discussion is subject to
some caveats about the effects of disordered regions in the
crystal.
Key words
Protein precision, Luzzati plots, Restrained refinement