[phenixbb] problem refining Fe-S cluster

Nathaniel Echols nechols at lbl.gov
Fri Jul 5 07:49:22 PDT 2013

Setting the B-factors manually usually isn't a great solution.  I
would suggest either a) refining the occupancies for each cluster, or
b) refining anomalous scattering factors for the irons.


On Fri, Jul 5, 2013 at 7:40 AM, Edward A. Berry <BerryE at upstate.edu> wrote:
> I have a problem refining a structure with iron-sulfur clusters. The irons
> refine
> to low B-factors (~25 in this case, while wilson B and B-average are around
> 45
> and the Sg's ligating the irons are ~30).  The irons have negative
> difference density
> and there is positive density in the center of the cluster (not on the S as
> it appears;
> the S is actually above the plane of the irons and the positive density
> below).
> (see attached map)
> It's possible that the cluster is lost in some percent of the molecules, and
> I
> could refine occupancy to get rid of the negative density, but I suspect
> this is
> likely to be because the B-factors are too low. I will try manually setting
> B
> for the Fe's and refining without ADP step, but does anyone have a better
> suggestion?
> This was refined for one macrocycle with
>     strategy = *individual_sites individual_sites_real_space rigid_body \
>                *individual_adp group_adp tls *occupancies group_anomalous
> thanks,
> eab
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