Wilson plot

relationship of Wilson B and Mean B factor

Dirk Kostrewa explains: at higher resolution, the Wilson plot captures mainly the contribution of atoms with lower B-factors which leads to a systematic underestimation of the true B-factor distribution. Accordingly, the average B-factor of refined structures tends to be higher than the Wilson B-factor.

Pavel Afonine found:

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 was computed using phenix.model_vs_data which uses "likelihood based wilson scaling"
• Average_B was 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%.

This is where the likelihood based wilson scaling comes from:

A.N. Popov and G.P. Bourenkov "Choice of data-collection parameters based on statistic modeling" Acta Crystallogr. (2003). D59, 1145-1153

Notes related to this are at [1]