[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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



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


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
 _______________________________________