Re: free-atom refinement

[Norbert Straeter <strater@chemie.fu-berlin.de>]

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



I always refine metal ions unrestrained in order to obtain unbiased
metal-ligand distances. At 2.2 A resolution the B-value for a relatively
electron-rich atom as Fe should be well defined. As you suspect, the iron
site is most likely partially occupied (or occupied by e.g. Mg2+ ?) since
the surrounding ligands have significantly lower B-values.  
Same happened to us on a dizinc protein, with one of the zincs having a 
significantly higher B-value relative to the other neighboring zinc and
the ligands.
In our case data collected at the zinc white line were  available 
which also showed a significantly lower peak height for the Zn with the
higher B in an anomalous map.
I would leave things as they are and mention the possibility of a
partially occupied metal site in the paper. You could set the B to 30 and
refine the occupancy to get an estimate of the occupancy. 

-Norbert


On Fri, 11 Sep 1998, Thomas Gleichmann wrote:

> Dear all
> 
> A general question of policy regarding occupancy refinement/free-atom
> refinement.
> 
> In my current (Rfree:29.6, R-work:21.7, res:2.2A; with N, C terminus and
> a loop disordered) model of  a non heme-Fe protein I'm somewhat puzzled
> by the fact that ligands have sensibly low-B values (HIS=29, other
> HIS=21, GLU=36, H2Os=25) which is much lower than Fe=65, I suspect
> occupancy <1 for Fe? (XPLOR with bulk solvent correction,ARP, Refmac,
> refinement cycles were used).
> I'm interested to get as close as possible to "unbiased", "true"
> ligand-metal distances as I'd like to compare them with EPR data.
> 
> Comments from people with similar problem of performing an unrestrained
> refinement are greatly appreciated.
> 
> Thanks in advance,
> Thomas
> 
> -- 
> Dr. Thomas Gleichmann
> St. Vincent's Institute of Medical Research
> 9 Princes Street, Fitzroy,
> Victoria 3065,Australia
> Phone:  +61-3-9288-2491
> Fax:    +61-3-9416-2676
> email: thomas@shiner.medstv.unimelb.edu.au
>