[phenixbb] amazing good statistics

[Pavel Afonine]

Hi Christian,

this is kind of Rwork/Rfree that you would get if you take a very high 
resolution structure, may be 1.2-1A and higher, cut the data off at 
2.2A, and refine it again.
So one explanation is that your crystals could probably diffract to a 
higher resolution...

The command

phenix.r_factor_statistics 2.2

gives typical R-factors at around 2.2A resolution are:

Histogram of Rwork for models in PDB at resolution 2.10-2.30 A:
      0.115 - 0.137      : 9 <<< you are here
      0.137 - 0.159      : 121
      0.159 - 0.182      : 703
      0.182 - 0.204      : 1637
      0.204 - 0.226      : 1749
      0.226 - 0.248      : 735
      0.248 - 0.270      : 147
      0.270 - 0.293      : 12
      0.293 - 0.315      : 2
      0.315 - 0.337      : 2
Histogram of Rfree for models in PDB at resolution 2.10-2.30 A:
      0.157 - 0.181      : 20 <<< you are here
      0.181 - 0.205      : 163
      0.205 - 0.229      : 784
      0.229 - 0.253      : 1733
      0.253 - 0.277      : 1617
      0.277 - 0.301      : 671
      0.301 - 0.325      : 101
      0.325 - 0.349      : 22
      0.349 - 0.373      : 5
      0.373 - 0.397      : 1
Histogram of Rfree-Rwork for all model in PDB at resolution 2.10-2.30 A:
      0.001 - 0.011      : 47
      0.011 - 0.021      : 176
      0.021 - 0.031      : 533
      0.031 - 0.041      : 997 <<< you are here
      0.041 - 0.050      : 1306
      0.050 - 0.060      : 1062
      0.060 - 0.070      : 602
      0.070 - 0.080      : 216
      0.080 - 0.090      : 113
      0.090 - 0.100      : 65
Number of structures considered: 5117

Pavel


On 4/3/12 9:59 AM, Christian Roth wrote:
> Dear Phenix people,
>
> is there a major improvement in the algorithm? I have refined a 2.2 Ang. room
> temperature dataset with very good data statistics (I think)
> Rmerge  3.7%(8.9%)
> completeness  96%(92%)
> I/sigI  16,6(8,8)
> in parentheses are the values for the highest resolution shell.
>
> After refinement I have a R/Rfree of 0.1294/0.1670.
> In some shells there are values close to 0.100 and in the lowest shell Rfree
> is lower than Rwork.
> The quality of the data are really quite good, what is probably one of the
> reasons,  but I am close or below to the border of the Range of R values in
> the pdb. Great for me, but I wanna be sure that it is really true.
> It was a MolRep with a close homolog, but I run a torsion angle sim annealing
> to decouple R/Rfree and the MolRep was done with an poly-Ala model to prevent
> too much model bias.
>
> Best Regards
>
> Christian
>
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