[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"
>
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>
>
>
> -- 
> -----------------------------------------------------------------
> 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
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