Problems with EXAFS Fitting of Metalloprotein Zinc Samples
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
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 temperatures (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... cheers, Robert 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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Carolyn, Robert and Bruce have given you excellent answers already, so I'll pile in on more specific questions. I take it you are seeing this for all Zn samples, e.g., Zn with just N/O ligands as well as mixed N/S? What if you fit data for some standard coordination complex like Zn(imid)6, which you know is a definite Zn-N6 site? Zn EXAFS is a little outside my wheel-house, but in my experience my best fits always had <6 first shell scatterers for Zn sites. I am under the impression that good fits to mixed N/S sites are challenging to fit since the Zn-N and Zn-S scattering are out of phase with each other. Bond valence sums might come in handy as a sanity check if you are trying to justify a 4C site over 6C, although it doesn't handle geometric distortions very well (not likely to be an issue in your case). Have a look at Thorp, Inorg. Chem. 1992, 31, 1585-1588 DOI: 10.1021/ic00035a012 and Liu&Thorp, Inorg. Chem. 1993, 32, 19, 4102-4105, 10.1021/ic00071a023. Be aware that there is an error in the table in the first paper: the r0 values for Zn-O and Zn-S are transposed. Unfortunately a Zn-S r0 isn't given, but you might find one going back to the parent Brown & Altermott reference or alternatively can interpolate from Cu and Ni values. Just an idea, Erik -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Carolyn Carr Sent: Monday, November 9, 2015 1:24 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples 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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
On 11/11/2015 08:52 AM, Farquhar, Erik wrote:
Bond valence sums might come in handy as a sanity check if you are trying to justify a 4C site over 6C, although it doesn't handle geometric distortions very well (not likely to be an issue in your case). Have a look at Thorp, Inorg. Chem. 1992, 31, 1585-1588 DOI: 10.1021/ic00035a012 and Liu&Thorp, Inorg. Chem. 1993, 32, 19, 4102-4105, 10.1021/ic00071a023. Be aware that there is an error in the table in the first paper: the r0 values for Zn-O and Zn-S are transposed. Unfortunately a Zn-S r0 isn't given, but you might find one going back to the parent Brown & Altermott reference or alternatively can interpolate from Cu and Ni values.
Really excellent point! Artemis has a few ways of integrating bond valence sums into the workflow: http://bruceravel.github.io/demeter/artug/extended/bvs.html B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
participants (4)
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Bruce Ravel -
Carolyn Carr -
Farquhar, Erik -
Robert Gordon