Hi,

1. do you know for sure that you have useful Se incorporation levels (i.e. by MS)?

2. there are minimal distance constraints on how close heavy atoms may be (one could use general chemistry knowledge to figure them out). Two actual Se atoms should never be as close as 1A apart. The sites can appear to be this close if you’re dealing with disorder (but then occupancies will be a giveaway) or with a twinned crystal (in both cases the actual atoms aren’t really 1A apart but they appear to be) – and in the latter case all bets are off. Did you thoroughly check for twinning? Based on your knowledge of the enzyme in question – is there anything funky like a possible sulfur-iron cluster, metal ion coordination, etc.?

3. I am not sure how to interpret your comments regarding resolution and anomalous signal quality – 1.6A is certainly nice (assuming that you and I use the same terms to describe ‘good quality’) and to be honest useful anomalous signal to 2.2A is also quite nice.

4. Returning to the choice of space group – are you sure it’s P21? There is such a thing as a P2 protein crystal although the instance of that SG is quite rare (95 entries in the current PDB) in the protein world. Again, I would take another close look at twinning possibilities.

Good luck,

Artem

“Nothing is built on stone; all is built on sand, but we must build as if the sand were stone”

 Jorge Luis Borges

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From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of yang li
Sent: Tuesday, July 28, 2009 10:10 PM
To: [log in to unmask]
Subject: [ccp4bb] Deal with close heavy atom sites?

Dear all,

      I have a 1.6A data in P21 spacegroup whith good quality, wich is assumed to contain 4 Set-Met. But the patterson map

appears strange. There is a very big heavy peak in the harker section, and seems like an irregular ellipse, while there are small

peaks very near(almost connect) to this big peak and the origin, say about 0.05 in fraction, looks like cross peaks.It looks like the

heavy atoms are very close if there are more than one. I tried several programs and many heavy atom coordinates sits, but none

of them can solve it. Shelxd got a set of sites looks best with set the minimum distance to 1A, since the patterson map from it

looks like the experimental patterson map, though not very much. But with this HA sites can get nothing meaningful. By the way,

it is a small molecule with no more than 150 residues, one molecule/ASU. According to shelxc the signal is not strong, can only

be used to aroud 2.2A.

     Any suggestions would be appreciated!