What leads you to believe Rfree is too high? - without knowing your data/parameter ratio it's impossible to tell. If you look at our paper Acta Cryst. (1998). D54, 547-557 (see Fig 1), then calculate the ratio y = Rfree/Rwork: in this case it is 0.33/0.24 = 1.375. Now look at the curve labelled 'a=2' (for normal restrained isotropic refinement) for the theoretically expected ratio and the green dots for the observed ratios (structures in the PDB at resolutions between 2.0 and 2.5 A). Then you need to calculate the ratio x = (no of atoms in the a.u.) / (no of reflections in the working set) and see where the point (x,y) falls relative to the curve and the green dots. If it's on or near the curve and in the middle of the green dots it's fine, if not then we need to work out why.
-- Ian On Wed, Jul 13, 2011 at 4:38 PM, Careina Edgooms <careinaedgo...@yahoo.com>wrote: > Dear ccp4 bulletin board > > I just have a slight concern regarding my Rwork Rfree difference. I have a > structure that I have solved. I am reasonably content that it is complete > because it has refined well, it no longer has bad geometries and contacts > and all the rotamers, ramachandra, bond lengths etc are good. It gives > favourable scores on molprobity and procheck. My only concern is the R > factor difference. The resolution of the structure is 2.3A. The R factor is > 0.24 after refinement but the Rfree is 0.33 which seems to me to be rather > high. Should I be concerned? > > During refinement Rfree only drops from about 0.36 to 0.33 while the R > factor drops from 0.31 to 0.24.. I have removed automatic weighting in > refmac in order to constrain my bond lengths and angles during a couple of > rounds of refinement. This did not have any effect on the R factors, > however. I am fairly content that the space group I have chosen is correct > so I am not sure what else could cause the big difference in R factors? > There is no twinning. > > Can I be satisfied that my structure is correct despite the high R free or > should I be doing other checks/ trying other things before I can submit this > structure? > > Thank you for any help > Careina >
