Re: [ccp4bb] Differentiating bound Mn & Ca.

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From: Sreeram Mahesh mahesh {- at -} PHYSICS {- dot -} IISC {- dot -} ERNET {- dot -} IN
Date: 2007-04-16

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Subject: Re: Differentiating bound Mn & Ca.
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-04-16

Subject: Re: Differentiating bound Mn & Ca.
From: Jim Pflugrath jim {- dot -} pflugrath {- at -} RIGAKU {- dot -} COM
Date: 2007-04-16

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
>> ).
>> 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

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

Previous message:
Subject: salt or protein?
From: Sreeram Mahesh mahesh {- at -} PHYSICS {- dot -} IISC {- dot -} ERNET {- dot -} IN
Date: 2007-04-16

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Subject: Re: Differentiating bound Mn & Ca.
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-04-16