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Re: [ccp4bb]: High and low B-factors
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On Thu, 28 Nov 2002, Eleanor J. Dodson wrote:
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> Ralf Bienert wrote:
> >
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> > Hello everybody!
> >
> > I solved a SAD structure to 1.8 A of a Se-Met protein and refine it with
> > refmac5.
> > However, I observed negative difference density around my Se-sites,
> > together with high B-factors of this atoms. I think this is due to
> > radiation damage. So far it is interpretable.
> > But why do I have so low B-values for my CE atoms, even lower than the
> > B-value of the other atoms of Se-Met.
> > My question now is how to interprete this observation and how to deal with
> > it. I just set the occupancy of both atoms to lower (same) values to get
> > rid of the negative difference density, but is this the right way???? Of
> > course, the B-value decresed, as well of CE.
> >
> > To get an idea I list my "worst" data (occupancy=1, B-value):
> >
> > N MSE 1.00 45.98 N
> > CA MSE 1.00 45.15 C
> > CB MSE 1.00 43.74 C
> > CG MSE 1.00 44.29 C
> > SE MSE 1.00 49.38 SE
> > CE MSE 1.00 9.79 C
> > C MSE 1.00 43.49 C
> > O MSE 1.00 44.28 O
> >
> > N MSE 1.00 25.08 N
> > CA MSE 1.00 25.90 C
> > CB MSE 1.00 25.00 C
> > CG MSE 1.00 29.97 C
> > SE MSE 1.00 35.56 SE
> > CE MSE 1.00 19.57 C
> > C MSE 1.00 24.97 C
> > O MSE 1.00 23.98 O
> >
> > Thanks in advance.
> > Ralf
>
>
> You dont say the wave length but the default formfactor for SE will not
> have any f' modification, so the B factor is trying to correct for that
> I guess..
>
> Why your CE B factor is so low is so low I cant think - Eleanor
>
Hi,
The wave length is 0.9393 A, the F'=~ 2.3. It is not that much but maybe
I have to consider a correctur of fo in refmac.
RALF