[phenixbb] pdb deposition

[Pavel Afonine]

Hi Sneha,

typical R-factors at this resolution are (using 
"phenix.r_factor_statistics 1.9" command):

Histogram of Rwork for models in PDB at resolution 1.80-2.00 A:
      0.093 - 0.118      : 4
      0.118 - 0.143      : 216
      0.143 - 0.168      : 2142
      0.168 - 0.193      : 5011
      0.193 - 0.218      : 3592
      0.218 - 0.243      : 1090  <<< your case
      0.243 - 0.268      : 151
      0.268 - 0.293      : 20
      0.293 - 0.319      : 1
      0.319 - 0.344      : 3
Histogram of Rfree for models in PDB at resolution 1.80-2.00 A:
      0.138 - 0.163      : 40
      0.163 - 0.189      : 651
      0.189 - 0.214      : 3178
      0.214 - 0.240      : 4512
      0.240 - 0.265      : 2809 <<< your case
      0.265 - 0.290      : 854
      0.290 - 0.316      : 159
      0.316 - 0.341      : 22
      0.341 - 0.367      : 3
      0.367 - 0.392      : 2
Histogram of Rfree-Rwork for all model in PDB at resolution 1.80-2.00 A:
      0.000 - 0.010      : 97
      0.010 - 0.020      : 683
      0.020 - 0.030      : 2367
      0.030 - 0.040      : 3800 <<< your case
      0.040 - 0.050      : 3085
      0.050 - 0.060      : 1422
      0.060 - 0.070      : 511
      0.070 - 0.080      : 172
      0.080 - 0.090      : 73
      0.090 - 0.100      : 20
Number of structures considered: 12230

..so, in terms of R-factors your are fine.

Run Comprehensive validation in Phenix GUI and check all "red flags". I 
would say you need to be able to explain rotamer/Ramachandran outliers 
or fix them otherwise.

Pavel



On 10/24/14 11:50 AM, Sneha Rangarajan wrote:
>
> Hi everyone,
>
> For a 1.9A dataset, here are my statistics-
>
> Rfactors: 22/26
>
> Ramachandran favored: 90.60%
>
> Ramachandran outliers: 2.17%
>
> Rotamer outliers: 4%
>
> Clashscore: 8
>
> Bonds: 0.007
>
> Angles: 1.2
>
> I have tried a couple of things to refine it further but nothing seems 
> to improve all the parameters.
>
> My question is what is an acceptable Rfactor at this resolution for 
> deposition in pdb?
>
> Thanks,
>
> Sneha
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20141024/12346da5/attachment.htm>