Resolution is 1.5A, Wilson B is 11.8. Does that mean that might values are more than within expected ranges? I knew at this resolution B factors are considerably lower, but I was suspicious that some seemed, so low, specially after recent problems of over refinement of B factors with another protein at 1.7A...
Must admit I never had such nice structures before, so I was being extra careful. Paula On 23 November 2010 19:27, Ethan Merritt <merr...@u.washington.edu> wrote: > 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 > > > >
