> I'm refining a structure with 8800 independent reflections (81.4% completeness)
> and resolution limit 2.32 A. In my model I now have all residues and 53
> water molecules. The R-factor is 0.172 and R-free is 0.265 (at 2.32 A).
> When I add waters both R and R-free decrease, but during refinement
> (positional) only R decreases. When should I stop refinement? Right now or
> when R-free doesn't decrease when adding waters?
>
> Thanks,
>
> Peter
The R values decreases but R-free not (may be goes up a bit)
that indicates you added too many waters. The model and
electron density map would not be improved if R value decreases only
- you have to stop refinement and check those waters.
The adding waters should be judged by the R-free during or
after refinement NOT at the beginning of refinement.
Conventionally the total number of
waters can be approximate to the number of residues. But we found that
is not really true. We suggest that only build in the bonded waters
and very decent waters - about 1/3 number of residues, and then,
do the bulk solvent refinement, which improves R-free.
! References:
!
! 1. Jiang, J.-S. & Brunger, A.T. (1994).
! "Protein Hydration Observed by X-ray Diffraction: Solvation
! Properties of Penicillopepsin and Neuraminidase Crystall Structures"
! J. Mol. Biol., 243, 100-115.
Jiansheng Jiang.
