On Tuesday 31 March 2009 09:57:13 Jose Antonio Cuesta-Seijo wrote:
> Hi!
>
> Normally the cell parameters, etc change very very little. You'll
> only know if the bromides got in at the synchrotron by looking at the
> fluorescence spectrum
That won't help, normally. It only tells you that there is bromide in
the solution, not that it found ordered positions in your crystal.
> and at the anomalous signal. Normally some will
> make it in and some will be in ordered sites, then it becomes mostly
> a question of data quality to detect it.
Right. You have to process the data and look for a real signal.
The mere presence of Br is not enough.
In my experience, the frustrating thing is that even if the Br soak
"works" in the sense that it introduces Br into your lattice, the
signal is often/usually not sufficient to phase the structure
de novo. Nevertheless, when you eventually do solve and refine
the structure, you can go back to your anomalous difference data
and calculate a Bijvoet Difference Fourier that clearly shows the
Br sites.
Ethan
> You could also try the equivalent iodide soak. Iodine has a decent
> anomalous signal at the copper wavenght and thus the anomalous signal
> can be detected at your home source and many times the structure can
> be solved by SAD or SIRAS. I would also thing that conditions that
> give ordered iodide sites are likely to result in ordered bromide
> sites, although the ions are not identical.
>
> Jose.
>
>
> **************************************
> Jose Antonio Cuesta-Seijo
> Cancer Genomics and Proteomics
> Ontario Cancer Institute, UHN
> MaRS TMDT Room 4-902M
> 101 College Street
> M5G 1L7 Toronto, ON, Canada
> Phone: (416)581-7544
> Fax: (416)581-7562
> email: jcue...@uhnres.utoronto.ca
> **************************************
>
>
>
> On Mar 31, 2009, at 12:19 PM, tat cheung cheng wrote:
>
> > Hi all
> >
> > I am now trying to do bromide soaking, but i am not really sure
> > does the bromide atom enter my crystal. So is there any signs that
> > indicate the entry of bromide atom? e.g. does the space group, cell
> > dimension change? or just nothing change, and the bromide atom just
> > get in?
> > Thanks very much.
> >
> > T.C. Cheng
> >
> >
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>
>
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
