Re: [ccp4bb] Metal-ligand(s) positioning following refinement...

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Metal-ligand(s) positioning following refinement...
From: James Pauff pauffjm {- at -} YAHOO {- dot -} COM
Date: 2007-07-11

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Subject: Re: Metal-ligand(s) positioning following refinement...
From: Edward Snell esnell {- at -} HWI {- dot -} BUFFALO {- dot -} EDU
Date: 2007-07-11

Hi James,

I've seen something similar with another metal site. It may be that the
X-rays have photoreduced the metal and you may have a different
coordination from that seen from the EXAFS data (recorded at much lower
dose). A good example is Yano et al. PNAS 102, 12047-12052, X-ray damage
to the Mn4Ca complex in single crystals of photosystem II: A case study
for metalloprotein crystallography. It's a good example of the problem.
Other studies are out there with similar effects send for Fe and Cu.

Cheers,

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Email: esnell@hwi.buffalo.edu Telepathy: 42.2 GHz

Heisenberg was probably here!

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Email: esnell@hwi.buffalo.edu Telepathy: 42.2 GHz

Heisenberg was probably here!

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
James Pauff
Sent: Wednesday, July 11, 2007 9:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Metal-ligand(s) positioning following refinement...

Good day all,

I have a metal center in my enzyme active site, in a
roughly square pyramidal coordination. I know from
EXAFS and other work how this coordination sphere
should look, but following REFMAC the cofactor here
does not end up realistically coordinated/oriented.
Although it is in the density and roughly in position,
the coordination sphere and ligands are not correct,
and not correctly connected.

Is there a means by which I can position this
cofactor, establish the connectivity I want, and then
specifically restrain this cofactor/center while
refining?

Thank you,
Jim

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Metal-ligand(s) positioning following refinement...
From: James Pauff pauffjm {- at -} YAHOO {- dot -} COM
Date: 2007-07-11

Next message:
Subject: Re: Pymol, labels, maps
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-07-11