[Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

Robert Gordon ragordon at alumni.sfu.ca
Mon Nov 9 16:33:18 CST 2015

Hi Carolyn,

Do you see this behaviour even for standard samples, where the local 
co-odination of the
zinc is known? If this is only happening for unknowns, then it could be 
telling you
that you have heavier or more scatterers present than you have included 
in your fitting model.

So^2, N and sig^2 are strongly correlated (So^2 and N directly for a 
1-shell fit).
Have you tried breaking the correlation by measuring at different 
(changes sig^2, not N)?

In the EXAFS section of the Encyclopaedia of Molecular Biology, it 
discusses difficulties
in analysing Zn metalloproteins due to not including 
multiple-scattering. If a MS peak
is leaking or lurking under the first shell peak(s), there is additional 
intensity that the fitting might
try to compensate for by increasing N (and would depend on the strength 
of the MS peak, which is,
in turn, dependent on local geometry).

...just some initial thoughts...


On 11/9/2015 10:24 AM, Carolyn Carr wrote:
> Hi,
> I have a general question rather than specific. I have only ever fit 
> XAS data on metalloproteins and one feature that I see is that when 
> fitting Zinc samples in R-space there is no local minima. For Cobalt 
> and Nickel samples I typically get one or a few fits that are 
> obviously significantly better in R-factor (with reasonable distances, 
> sigma^2, etc) but for Zinc this is not the case.
> I can get many good fits and Zinc likes to increase the coordination 
> up to 8 for all data sets I have ever fit, although there is obviously 
> no physical basis in this. This is true of not just my own proteins 
> but Zinc samples made by collaborators, and after looking through 
> previous group members fit tables, they had similar issues.
> My understanding is that one of the benefits of fitting in R-space is 
> that there is a local minima, whereas in k-space there are many 
> minima. I was wondering if there was a physical basis for this feature 
> in Zinc samples, or if perhaps my group is not aware of some 
> experimental setup that we should be doing for Zinc that would resolve 
> this problem.
> Thank you for any help regarding this matter,
> Carolyn Carr
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