[phenixbb] high average b-factor vs. Wilson B
Pavel Afonine
pafonine at lbl.gov
Tue Aug 3 23:06:32 PDT 2010
Typical R-factors for structures at around 1.45A are:
phenix.r_factor_statistics 1.45
Histogram of Rwork for models in PDB at resolution 1.35-1.55 A:
0.092 - 0.122 : 40
0.122 - 0.152 : 344
0.152 - 0.183 : 743
0.183 - 0.213 : 722 <<< your structure
0.213 - 0.243 : 206
0.243 - 0.273 : 18
0.273 - 0.303 : 3
0.303 - 0.334 : 0
0.334 - 0.364 : 1
0.364 - 0.394 : 1
Histogram of Rfree for models in PDB at resolution 1.35-1.55 A:
0.113 - 0.148 : 18
0.148 - 0.183 : 333
0.183 - 0.217 : 982
0.217 - 0.252 : 607 <<< your structure
0.252 - 0.287 : 125
0.287 - 0.322 : 10
0.322 - 0.357 : 1
0.357 - 0.391 : 0
0.391 - 0.426 : 0
0.426 - 0.461 : 2
Histogram of Rfree-Rwork for all model in PDB at resolution 1.35-1.55 A:
0.001 - 0.011 : 82
0.011 - 0.020 : 476
0.020 - 0.030 : 666 <<< your structure
0.030 - 0.040 : 381
0.040 - 0.050 : 246
0.050 - 0.059 : 121
0.059 - 0.069 : 70
0.069 - 0.079 : 26
0.079 - 0.088 : 4
0.088 - 0.098 : 6
Number of structures considered: 2078
So, your R-factors look quite normal given the resolution.
Regarding Wilson vs Average B-factors, here is the statistics over PDB:
Resolution_range Wilson_B Average_B Number_of_structures
0.00 - 1.00 9.77 13.11 94
1.00 - 1.25 10.58 16.44 401
1.25 - 1.50 13.50 19.14 1050
1.50 - 1.75 17.20 21.76 3600
1.75 - 2.00 22.27 26.82 5510
2.25 - 2.50 35.70 39.42 3385
2.50 - 2.75 43.71 44.73 2844
2.75 - 3.00 53.86 51.94 1628
3.00 - 3.25 65.11 60.76 780
3.25 - 3.50 81.69 78.70 165
3.50 - 3.75 92.67 88.84 100
3.75 - 4.00 111.83 102.29 30
(*) Wilson_B is computed using phenix.model_vs_data
Average_B is computed using phenix.model_vs_data from PDB file
(TLS is accounted for)
Structures selected such that the recomputed R-factor matches the
one in PDB file header within 1%.
As you see, your B-factors are quite high. Should you worry about it? I
don't know. If everything else is done right and look good (as good as
R-factors), then no, otherwise I would think what might be the cause for
this. Although it's interesting to know why this happens. I will
probably look at the histogram of Wilson B and average B around this
resolution to see what people had in the past.
Pavel.
On 8/3/10 10:48 PM, Peter Zwart wrote:
> If you did use aniso B and are stuck at 19.8% for a 'true' 1.45 A data
> set, I suspect that something might be off ....
>
> did you check possibilities for twinning?
>
> did you optimize weights properly?
>
> P
>
>
>
>
>
>
> 2010/8/3 Geoffrey Feld <gkfeld at berkeley.edu <mailto:gkfeld at berkeley.edu>>
>
> Dear PhenixBBers,
>
> I'm working on a 1.45 A structure I solved using MR (phaser) and
> I'm pretty close to finishing, just plopping in waters and fixing
> rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because
> my Wilson B is 27.00 while my average B for macromolecule is more
> like 43, and for solvent is 48. I have enough data to use
> anisotropic ADP refinement, which was a big help in bringing down
> the Rfree, but the average B hasn't really moved much. Should I be
> concerned about this? Should I try adjusting the wxu, or some
> other parameter?
>
> Thanks!
> --
> Geoffrey K. Feld
>
> Department of Chemistry
> 492 Stanley Hall
> University of California, Berkeley
>
> "Vigilia pretium libertatis"
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
> --
> -----------------------------------------------------------------
> P.H. Zwart
> Research Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
> BCSB: http://bcsb.als.lbl.gov
> PHENIX: http://www.phenix-online.org
> SASTBX: http://sastbx.als.lbl.gov
> -----------------------------------------------------------------
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100803/d126a3ba/attachment-0003.htm>
More information about the phenixbb
mailing list