[ccp4bb]: Re: [sharp-discuss] Phasing with FeS cluster

[Ricardo Aparicio <aparicio@if.sc.usp.br>]

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Dear Paul,

	 
	I think you have biological information to confirm the 4Fe-4S cluster
hypothesis. Anyway, how far from each other your sites are? Is it
possible to have only one site instead? Maybe this could be an effect of
anisotropy. A good idea is to refine again using only the best site and
do a peak search in the Sharp residual maps. If you have more peaks,
after processing them, they should not be present in the residual maps. 
	Yet you have "low" resolution, after refining isotropic B-factors you
could try to refine anisotropic B-factors, maybe it helps. I would check
Truncate output to see if you have anisotropy in your data. Maybe the
shifts in coordinates can be coincident with an anisotropic behaviour in
a preferential direction (y direction??). I wouldn't refine f' neither
f'' unless you have reliable anomalous signal.
	This refers to old Sharp version (not automatic).
	
	Hope it helps you.


Cheers,

Ricardo Aparicio
PhD Student - USP- Sao Paulo
Brazil  

PS: 
- How many eingenvalues filtered out? 
- Scaling OK? (nice scripts in the SCALA manual)
- do you have non-isomorphism (in-house native, did crystals die during
data collection?)?
- to asses anomalous signal I use to have a look on "Histograms and
statistics on squared anomalous differences" in the Sharp logfile.



##############################################################################
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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