Hi Careina,
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?
>
looking at all similar to yours structures in PDB (*):
phenix.r_factor_statistics 2.3
Histogram of Rwork for models in PDB at resolution 2.20-2.40 A:
0.126 - 0.147 : 29
0.147 - 0.168 : 253
0.168 - 0.189 : 958
0.189 - 0.210 : 1649
0.210 - 0.232 : 1440
0.232 - 0.253 : 549 <<< your structure
0.253 - 0.274 : 125
0.274 - 0.295 : 12
0.295 - 0.316 : 1
0.316 - 0.337 : 4
Histogram of Rfree for models in PDB at resolution 2.20-2.40 A:
0.165 - 0.188 : 31
0.188 - 0.211 : 223
0.211 - 0.235 : 860
0.235 - 0.258 : 1733
0.258 - 0.281 : 1508
0.281 - 0.304 : 542
0.304 - 0.328 : 97
0.328 - 0.351 : 19 <<< your structure
0.351 - 0.374 : 6
0.374 - 0.397 : 1
Histogram of Rfree-Rwork for all model in PDB at resolution 2.20-2.40 A:
0.001 - 0.011 : 53
0.011 - 0.021 : 172
0.021 - 0.031 : 524
0.031 - 0.041 : 960
0.041 - 0.050 : 1264
0.050 - 0.060 : 1050
0.060 - 0.070 : 592
0.070 - 0.080 : 224
0.080 - 0.090 : 114
0.090 - 0.100 : 67 <<< your structure
Number of structures considered: 5020
(*): *Crystallographic model quality at a glance*. Acta Cryst. D65, 297-300
It seems like you should be concerned about the high Rfree and Rfree-Rwork.
The second question about how to address it is program specific in some
sense and I hope Refmac experts will address it.
Pavel.
