Although the peak height of S atoms can be used as an internal yardstick,
one has to worry about differences in occupancy and possibly hetergeneous
sites (i.e. Ca, Mn and Mg) which can confuse the interpretation of the
results.
On Mon, 16 Apr 2007, Eleanor Dodson wrote:
In cases like this I use the S atoms to calibrate the peak height.
Of course it isnt definitive a) it is near the noise level, and b) peak
height is very dependent on B factor..
But the ratio might distinguish between an atom with an f" of 1.3 or f"=2.8
Eleanor
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
<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
--
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David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net <http://www.dbriggs.talktalk.net>
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