This is a perennial Q, and one without a good answer.
There are some pretty uncontriversible facts.
If you have atomic resolution your R and Rfree will be pretty close -
90-95% of data gives you a pretty well correct structure and the FreeR
will reflect that..
If you have low resolution and you get the spacegroup wrong - eg call
P3122 P31 and assign the FreeR set without taking account of the extra
symmetry your R and Rfree will be pretty close! but that doesnt mean
you have a better structure..
If you have non-crystallographic symmetry the effects are uncertain, but
in many cases this too gives you a lower than expected FreeR value, and
again, that doesnt mean you have a better structure..
In general the difference in R and Rfree should be correlated with the
resolution, but there doesnt seem to be any absolute level of
expectation; thee are toomany other variables to consider..
Eleanor
Pavel Afonine wrote:
Hi Sivia,
you say the resolution is 1.8A, and your R-work=0.19 and R-free=0.27.
Here is the distribution of R-factors for structures in PDB deposited at similar
resolution (in range between 1.75A and 1.85A):
Histogram of Rwork for all model in PDB at resolution 1.75-1.85:
0.114 - 0.130 : 6
0.130 - 0.147 : 48
0.147 - 0.163 : 221
0.163 - 0.180 : 484
0.180 - 0.196 : 718 <<< your structure
0.196 - 0.212 : 508
0.212 - 0.229 : 271
0.229 - 0.245 : 105
0.245 - 0.262 : 20
0.262 - 0.278 : 7
Histogram of Rfree for all model in PDB at resolution 1.75-1.85:
0.153 - 0.171 : 17
0.171 - 0.190 : 127
0.190 - 0.208 : 380
0.208 - 0.227 : 647
0.227 - 0.245 : 648
0.245 - 0.263 : 360
0.263 - 0.282 : 132 <<< your structure
0.282 - 0.300 : 64
0.300 - 0.319 : 10
0.319 - 0.337 : 3
Histogram of Rfree-Rwork for all model in PDB at resolution 1.75-1.85:
0.001 - 0.013 : 41
0.013 - 0.025 : 336
0.025 - 0.036 : 852
0.036 - 0.048 : 693
0.048 - 0.060 : 309
0.060 - 0.072 : 98
0.072 - 0.084 : 40 <<< your structure
0.084 - 0.095 : 11
0.095 - 0.107 : 4
0.107 - 0.119 : 4
You also mentioned you cut the data off (the actual resolution is 1.6A). Doing
so just to improve R-factor doesn't seem like a good idea.
Similar histograms for structures at around 1.6A resolution:
Histogram of Rwork for all model in PDB at resolution 1.55-1.65:
0.099 - 0.119 : 5
0.119 - 0.138 : 26
0.138 - 0.158 : 132
0.158 - 0.177 : 349
0.177 - 0.197 : 447 <<< your structure
0.197 - 0.217 : 281
0.217 - 0.236 : 129
0.236 - 0.256 : 17
0.256 - 0.275 : 6
0.275 - 0.295 : 1
Histogram of Rfree for all model in PDB at resolution 1.55-1.65:
0.137 - 0.156 : 6
0.156 - 0.175 : 45
0.175 - 0.195 : 208
0.195 - 0.214 : 391
0.214 - 0.233 : 395
0.233 - 0.253 : 200
0.253 - 0.272 : 96 <<< your structure
0.272 - 0.291 : 37
0.291 - 0.311 : 12
0.311 - 0.330 : 3
Histogram of Rfree-Rwork for all model in PDB at resolution 1.55-1.65:
0.001 - 0.010 : 27
0.010 - 0.019 : 217
0.019 - 0.029 : 374
0.029 - 0.038 : 350
0.038 - 0.047 : 233
0.047 - 0.056 : 106
0.056 - 0.065 : 49
0.065 - 0.075 : 23
0.075 - 0.084 : 10 <<< your structure
0.084 - 0.093 : 4
Pavel.
On 10/19/09 5:49 AM, Sylvia Fanucchi wrote:
> Web Bug from cid:[email protected]
>
> Dear all
>
> I have been refining my structure using refmac5 restrained refinement and the
> model currently has an R-factor of 0.19. What is concerning me is that there
> is quite a big discrepancy between the Rfree and the R-factor, with the Rfree
> being around 0.27. Furthermore, after about 10 rounds of refinement, the
> R-free actually starts to increase slightly although the R-factor continues to
> decrease. Does this mean that there is significant bias in my model? Does
> anybody know how I could go about addressing this problem?
>
> Thanks for any help J
>
> **Sylvia Fanucchi Ph.D**
>
> **Protein Structure-Function Research Unit**
> East Campus, Gate House Room 416
> School of Molecular and Cell Biology
> University of the Witwatersrand
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> South Africa
>
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