Dear all
I'm refining a 33kDa protein model and I have noticed that although all
other statistics seem fine, B factor values are quite low, with many around
7-10A2 and average overall values as follows.
Total number of atoms in chain A 2378
Average B value for main chain A 10.684
Average B value for side chain A 12.755
Average B value for whole chain A 11.665
Average rms B for 312 main chain residues 0.748
Average rms B for 273 side chain residues 1.777
These are values after anisotropic B refinement, with 1 TLS group in
refmac5. I get similar results if refinement is done without TLS (using
model + mtz before doing TLS refinement) and with
isotropic/overall/anisotropic B refinement and. Resetting B values to an
arbitrary high value (50 or 70) and rerunning refinement with all possible
options on/off also gives the same results.
Using Phenix, after resetting B values before refinement to arbitrary
values and with anisotropic or isotropic refinement, with or without
occupancy refinement also gives similar results.
As refinement of related molecules (but in different ligand bound states)
from similar quality crystals results in models with more realistic B
factors (as shown bellow), I strongly suspect that the B factors for this
protein have been over refined. However, I'm not sure what other refinement
settings to use to avoid this problem.
Total number of atoms in chain A 2352
Average B value for main chain A 20.651
Average B value for side chain A 21.815
Average B value for whole chain A 21.199
Any help and advice is most appreciated.
Best regards
Paula
========================================================
Dr Paula Salgado
Division of Molecular Biosciences
Department of Life Sciences
Faculty of Natural Sciences
Biochemistry Building, 5th Floor
Imperial College London
South Kensington Campus
SW7 2AZ
London
Tel: +44 (0)2075945464
Fax: +44 (0)20 7594 3057
