[sharp-discuss] Phasing with FeS cluster

[Clemens Vonrhein]

Paul,

I would have expected that at thsi resolution (2.6A for in-house) you
should be able to resolve the various Fe atoms in your Fe-S
cluster. How did you find your sites? Using Pattersons? Maybe it would
be a good idea to calculate some anomalous Pattersons at higher
resolution to see if you can resolve the Fe atoms.

If that's not possible, I would run SHARP at higher resolution, using
your best f'/f'' values and fixing all of these: in-house and remote
should be correct anyway. If you don't have a fluorescence scan for
your MAD data collection (and use CHOOCH to get f'/f'') I would take
the calculated ones. But careful: small changes in lambda can have
large effects in f'/f''. Use one of the MAD sites on the web to find
the f'/f'' values for peak and inflection.

After that SHARP run, the residual maps (ANO) should show additional
peaks if you used only a single Fe atom to refine the whole
cluster. From there you could bootstrap your way to add all additional
Fe (how many are there?).

I wouldn't go for tha U atom aproach ... sounds rather fishy to me ;-)

Hope that helps ... if not just post your SIN file to know what we're
discussing.

Cheers

Clemens

On Wed, Jan 09, 2002 at 10:22:45AM -0600, Paul Hubbard wrote:
> Hi all,
> 
> I am having trouble doing initial phasing for a protein with an FeS
> cluster. MAD data at the Fe abs. edge is to 3A, and in-house native
> anomalous is to 2.65A.
> 
> Due to the low resolution, I have been treating the 4Fe-4S cluster as a
> single Uranium atom. Therefore I use f' and f'' values for U taken from
> the Sasaki table. I fix these parameters for the in-house anomalous and
> remote wavelength data sets, and allow both f' and f'' to be refined for
> the inflection and peak wavelengths.
> 
> The problem is that the "y" coordinate moves by ~2A, and I get stupid
> final values for f' and f'' for the inflection and peak wavelengths
> (i.e., f' at inf. is 35.1671 and f'' is 10.405)
> 
> Any thoughts would be very much appreciated.
> 
> P.S: I have read the fancy-looking manual, and asked a number of people.
> No luck there.
> 
> AGS.
> 
> 
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