Re: [ccp4bb] how to improve Rfree?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: how to improve Rfree?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-10-19

Next message:
Subject: Re: how to improve Rfree?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-10-19

Subject: Re: how to improve Rfree?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-10-19

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:part1.00000305.09050909@lbl.gov
> >
> > 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
> > Johannesburg 2050
> > South Africa
> >
> > Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351
> > E-mail: Sylvia.Fanucchi@wits.ac.za
> >
> >
> >
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: how to improve Rfree?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-10-19

Next message:
Subject: Re: how to improve Rfree?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-10-19