Re: [ccp4bb] Differentiating bound Mn & Ca.

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CCP4bb <-- 2007 <-- April 2007 <-- 16 April 2007

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Subject: Differentiating bound Mn & Ca.
From: David Briggs bassophile {- at -} GMAIL {- dot -} COM
Date: 2007-04-16

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Subject: Re: Differentiating bound Mn & Ca.
From: Julie Bouckaert bouckaej {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2007-04-16

Subject: Re: Differentiating bound Mn & Ca.
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-04-16

David Briggs wrote:
> Dear all.
>
> I have recently solved a structure in-house, 2.8A, CuKa.
> I have a metal ion bound very obvious hepta-valent co-ordination, which
> would suggest either Ca or Mn.
> Neither was present in the crystallisation setup, but there was some Mg
> around, which has contaminants of both Ca & Mn.
> At 2.8A, I don't really think I can reliably discriminate between 2.15A
> & 2.36A distances to coordinating atoms
> (http://tanna.bch.ed.ac.uk/newtargs_06.html
> ).
> The B factors for refined Ca are 18, and Mn 30. The B-factors of
> coordinating atoms vary from... 18 > 30 - so no help there.
>
> I have a nice clear 6sigma anomalous difference peak, but then,
> according to http://skuld.bmsc.washington.edu/scatter/ both Ca (f" ~1.3)
> and Mn (f" ~2.8) scatter anomalously at that wavelength.
>
> The obvious solution is go to a synchrotron and scan around the Mn edge
> and see what happens, however, whilst waiting for beam time, is there
> any way I could... oh I don't know, use the peak in my anomalous
> difference Fourier to figure out what anomalous signal would be required
> to generate a peak of that size - a sort of back-transform???
>
> Is this do-able, and if so, how would one go about it?
>
> Cheers,
>
> Dave

Dave,

f" = 1.3 versus 2.8 sounds like quite a difference ... what is the anom peak
height of the sulfurs in your structure? The f" of sulfur at Cu Ka wavelength is
0.55 . So I'd expect the ratio of peakheights of your unknown metal divided by
the average peakheight of sulfurs (of roughly 18-30 A**2 B-factor) to give you
an idea of what you have. Of course this is no proof ...

Are there any other anom scatterers in your structure?

best,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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CCP4bb <-- 2007 <-- April 2007 <-- 16 April 2007

Previous message:
Subject: Differentiating bound Mn & Ca.
From: David Briggs bassophile {- at -} GMAIL {- dot -} COM
Date: 2007-04-16

Next message:
Subject: Re: Differentiating bound Mn & Ca.
From: Julie Bouckaert bouckaej {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2007-04-16