[Ifeffit] Debye Waller factors for Water Molecules

Paul Fons paul-fons at aist.go.jp
Mon Jul 30 05:31:48 CDT 2007


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
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