Hi Matt, I took a look at the paper you mentioned and as in my case, the water is appears to be pretty much only bonded to the Zn at 1.96 Angstroms for the isolated enzyme. I guess this implies that Anatoly's idea of using a Zn+2 solution as a starting point might make sense. I have no idea how much the DW varies for water in these types of systems. Is the usual idea to just set it at some "reasonable" value (e.g. from the idea of Anatoly) and then keep it fixed? Paul On Jul 30, 2007, at 3:51 PM, Paul Fons wrote:
Thanks everyone (Shelly, Matt, and Anatoly) for the info. I thought it would be fun to learn while trying to work out a (relatively) simple system. I have EXAFS data about a Zn site. The Zn is bonded to three cystedines so I have the DW pretty much under control, but for the water molecules. I will investigate the approaches mentioned here and see which one the data is most consistent with (I did have the foresight to choose a system for which I have high resolution x-ray crystallography data).
Thanks
Paul
On Jul 29, 2007, at 12:57 AM, Matt Newville wrote:
Hi Paul,
A. Vogel et al (Biochemistry 43, p10379, 2004) report a Zn water (or OH) at 2.0Ang with sigma2=0.007Ang^2 for data collected at 30K.
This is for a binuclear Zn compound, and the OH is a bridging ligand (with the other ligands being dominated by histidine-like rings), so I don't know how close it is to your structure. But it might be a good place to start.
Also, the results came from EXCURVE. That's not to suggest that the results are not reliable, but you might want to check carefully the meaning of sigma2. I'm not 100% sure of this (or what the Vogel et al paper is reporting), but I think the EXCURVE sigma2 might be a factor of 2 bigger than the Ifeffit sigma2.
I'd be a little wary of using an Einstein model for "water" ligands down to 30K. It would be interesting to hear how well an Einstein model compares to the DFT modeling for any ligands in a bio-molecule.
--Matt _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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