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 <[email protected]>

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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