Re: [ccp4bb]: High and low B-factors

[Ralf Bienert <bienert@mdc-berlin.de>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Hello!

I have ESI as well as MALDI-TOF mass spectra showing one peak (~8000 kD)
at the excepted mass for the Se-Met protein. So, I thought this is the evidence
for 100 % Se-Met incorporation. I also produced the protein in a
Met-auxotrophic strain.

Ralf


On Thu, 28 Nov 2002, Marko Hyvonen wrote:

>
> Are you sure you have 100 % Se-Met incorporation ? I would guess that if
> part of your seleniums are in fact sulfurs, modelling the as seleniums
> only would cause exactly what you describe now.
>
> Marko
>
>
>
> On Thu, 28 Nov 2002, Ralf Bienert wrote:
>
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > 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
> >
> >
> > *********************
> > Ralf Bienert
> > Crystallography Group
> > MDC-Berlin
> > *********************
> >
> >
>
>
>  ____________________________________
>
>  Marko Hyvonen, PhD
>  Department of Biochemistry
>  University of Cambridge
>  http://www-cryst.bioc.cam.ac.uk/~marko
>  tel:  +44-(0)1223-766 031 / 766 027
>  _______________________________________
>