[phenixbb] How to treat EDTA on a special position

Jan Gebauer jan.gebauer at uni-koeln.de
Tue Jun 25 02:12:41 PDT 2013

Dear all,

I recently solved a structure in R32/H (155).
Interestingly some crystal contacts are mediated by an Metal/EDTA complex.
The metal -presumably a magnesium- sits on a special position (x,0, 1/2)
in the middle of a twofold axis with the EDTA molecule coordinating it.
(See "top" view in dropbox image below)

If I fit the EDTA/Mg complex in the density, the symmetry will of course
generate a symmetry mate on the same spot. (see "side" view in dropbox  
image below). In
phenix.refine, both entities are refined, which of course gives wrongs

My question is, how to best define the Ligand to be compatible with
phenix.refine and -later- with pdb submission.
Should I just set occupancy to 0.5 for the whole EDTA molecule? - But then
I would still get two molecules at this site... Or split it somehow half
and let the second half be generated by symmetry? In that case, I would
need to define bonds over the asymmetric unit to prevent "dissociation" of
my ligand halves, wouldn't I? Or is there a third way?

I already searched the phenixBB, but only found some "old" threads
discussing vaguely similar problems. Unfortunately, they didn't help me to
answer which way is better... (or right...)



Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Otto-Fischer-Str. 12-14 / 50674 Köln
Fon: +49 (221) 470 3212	
Fax: +49 (221) 470 5066


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