problem refining Fe-S cluster
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
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.
-Nat
On Fri, Jul 5, 2013 at 7:40 AM, Edward A. Berry
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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Hi Ed, it looks like occupancies and B-factors need to be refined and refined until convergence. Also, if you apply any distance restraints for clusters (restrain Fe-S distances) make sure these restraints are correct. I've seen many cases like this and typically refining occupancy/b-factors and making sure restraints are correct solves the problem. I've never seen fixing specific parameters help and I can't understand logic for doing this. If you get stuck with this you can send me files off list and I'll have a look. Pavel On 7/5/13 7:40 AM, Edward A. Berry 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
participants (3)
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Edward A. Berry -
Nathaniel Echols -
Pavel Afonine