On Tuesday, November 23, 2010, Paula Salgado wrote: > 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,
What is the resolution? What is the Wilson B? > 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 >
