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Re: [ccp4bb] anomalous signal of Mn and Ca ions
 

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CCP4bb <-- 2008 <-- February 2008 <-- 29 February 2008
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Subject: Re: Off topic: General rule for maximum flow rate for affinity column?
From: "Mark J {- dot -} van Raaij" vanraaij {- at -} USC {- dot -} ES
Date: 2008-02-29 		Next message:
Subject: Re: anomalous signal of Mn and Ca ions
From: Johan Turkenburg jpt {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-29


Subject: Re: anomalous signal of Mn and Ca ions
From: Stephen Graham stepheng {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-29
As Ethan mentions, your best bet for an 100% positive ID would be to
collect a dataset above and below the Mn edge and see the anomalous
signal from the Mn atom disappear.

If that is not an option, there is a great paper by George Sheldrick
and friends regards using the Calcium Bond Valence Sum to determine
the nature of a metal based on its coordination geometry. [P. Müller,
S. Köpke and G. M. Sheldrick (2003) Is the bond-valence method able to
identify metal atoms in protein structures? Acta Cryst. D59, 32-37].

You could also have a look at one of my papers
where we applied this (and integration of the anomalous difference
density around the position of the scatterer, scaled against the
Sulfur signal of the Met's and Cys'es in the protein) to confirm metal
loading of a metalloenzyme [Graham, S, Bond, C, Freeman, H, Guss, J.
(2005) Structural and functional implications of metal ion selection
in aminopeptidase P, a metalloprotease with a dinuclear metal center.
Biochemistry.44: 13820-36]

Good luck,

Stephen

On 2/29/08, Sun Tang wrote:
> Dear All,
>
> In my structures, I want to assign Mn or Ca ions for some densities. But
> when I did not have anomalous density in CCP4i. I am not sure whether I was
> correct. The following was what I did:
>
> I processed the data with HKL2000 and select anomalous signal in scaling. In
> CCP4i, I selected "Run FFT-Creat Map" in the "Map& Mask Utilities". I select
> "O format to cover asymmetric unit" and "Plot section on Z axis from 0 to 1
> in steps on 10". All others were by default values. I display in ono10.
>
> I collected the data at the wavelength of 1 A. Do I need to adjust the
> wavelength to maximize the anomalous signal from Mn or Ca?
>
> Any ideas and suggestions are greatly appreciated!
>
> Sun Tang
>
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>
>


--
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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