Somewhat to our surprise, we have found that, even when the halide
signal is too weak to solve the substructure from scratch, when you
find the sites (in our case, by using the protein model as a
"substructure" in Phaser), they can still add significant phase
information. So you can get more out of it than just seeing which
sites are halides, especially since the model can be a rough and
incomplete one.
But if all you're after is seeing which sites are halides, the
procedure in Phaser (which is iterative, in that sites found in the
first round help to find further sites) is more sensitive and
convincingly finds more sites than an anomalous difference Fourier
(which is not iterative).
There's a tutorial on our web page with real (albeit lysozyme) data
illustrating how this works.
Regards,
Randy Read
On 31 Mar 2009, at 18:17, Ethan Merritt wrote:
> 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: [log in to unmask]
>> **************************************
>>
>>
>>
>> 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
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-
structmed.cimr.cam.ac.uk
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