Re: [phenixbb] high average b-factor vs. Wilson B

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 mailto:[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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