I agree that the difference in Rwork to Rfree is quite acceptable at
your resolution. You cannot/ should not use Rfactors as a criteria for
structure correctness.
As Ian points out - choosing a different Rfree set of reflections can
change Rfree a good deal.
certain NCS operators can relate reflections exactly making it hard to
get a truly independent Free R set, and there are other reasons to make
it a blunt edged tool.
The map is the best validator - are there blobs still not fitted? (maybe
side chains you have placed wrongly..) Are there many positive or
negative peaks in the difference map? How well does the NCS match the 2
molecules?
etc etc.
Eleanor
George M. Sheldrick wrote:
Dear Sun,
If we take Ian's formula for the ratio of R(free) to R(work) from his
paper Acta D56 (2000) 442-450 and make some reasonable approximations,
we can reformulate it as:
R(free)/R(work) = sqrt[(1+Q)/(1-Q)] with Q = 0.025pd^3(1-s)
where s is the fractional solvent content, d is the resolution, p is
the effective number of parameters refined per atom after allowing for
the restraints applied, d^3 means d cubed and sqrt means square root.
The difficult number to estimate is p. It would be 4 for an isotropic
refinement without any restraints. I guess that p=1.5 might be an
appropriate value for a typical protein refinement (giving an R-factor
ratio of about 1.4 for s=0.6 and d=2.8). In that case, your R-factor
ratio of 0.277/0.215 = 1.29 is well within the allowed range!
However it should be added that this formula is almost a
self-fulfilling prophesy. If we relax the geometric restraints we
increase p, which then leads to a larger 'allowed' R-factor ratio!
Best wishes, George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
