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Re: [ccp4bb] Differentiating bound Mn & Ca.
 

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CCP4bb <-- 2007 <-- April 2007 <-- 16 April 2007
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Subject: Re: Differentiating bound Mn & Ca.
From: Stephen Graham stepheng {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-04-16
Hi David,

You can use Sheldrick's Calcium Bond Valence Sum to descriminate
between metals (see Muller, P., Kopke, S., and Sheldrick, G. M. (2003)
Acta Crystallogr., Sect. D: Biol. Crystallogr. 59, 32-37) even at low
resolution. I have had good success with this method combined with
estimation of anomalous contribution scaled against the S atoms as
suggested by Kay.

Have a look at Graham, S. C., Bond, C. S.,
Freeman, H. C., and Guss, J. M. (2005) Biochemistry 44, 13820-13836.
 for plenty of examples. To do the anomalous
difference calculations I just integrated a 2x2x2 A box around the
metal atom and around the S atoms (in MAPMAN) then calculated the
ratio of anomalous difference...

Cheers,

Stephen

On 4/16/07, 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
>
> --
> ---------------------------------------
> David Briggs, PhD.
> Father & Crystallographer
> www.dbriggs.talktalk.net
> iChat AIM ID: DBassophile
> ---------------------------------------
> Anyone who is capable of getting themselves made President should on no
> account be allowed to do the job. - Douglas Adams


--
Dr Stephen Graham
Nuffield Medical Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549
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