On Tuesday, November 23, 2010, Paula Salgado wrote:
> Resolution is 1.5A, Wilson B is 11.8.
Right. So there you have it. The Wilson B is telling you straight from
the data that the expected B factors are on the order of 11.8
You reported your model as
> > > 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
So it looks like you're right on target.
Congratulations on a nice crystal, a nice data set, and a
promising model.
Ethan
>
> 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
> > >
> >
> >
>
