Re: [ccp4bb]: Phasing with FeS cluster

["David J. Schuller" <djs63@cornell.edu>]

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On Wed, 9 Jan 2002, Paul Hubbard wrote:

> 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.

even if you wanted to model this as a single atom, i don't see why you
would use the f' and f" values from U, these are dependent on the 
wavelength and the element and the edges for U are nothing like those for 
Fe, your dominant scatterer.  i would say use atom type Fe and let your 
occupancy go above 1.0.

but with 3.0 - 2.65 A you should be able to resolve the single atom 
positions.  you might try using a 4Fe-4S cluster from a known structure 
(if you are willing to presume its similarity) and run it through 
molecular replacement.  you might even give a shot at positioning the Fe 
atoms with direct methods.

if you are serious about wanting help, you might also disclose a few more 
details. for example, what software have you have been using?  that would 
enable experienced folk to toss in comments like "program X can't handle 
refining f' and f", try program Y instead".  what is your space group?  if 
your space group is monoclinic, any movement of Y could be laughed off.
some idea of the size of your asymmetric unit and how many 4Fe-4S clusters 
you expect to be present would also be very helpful.


cheers,

=======================================================================
"Now that I'm a cranky, constipated old man I can afford to say that
 the younger generation of scientists makes me sick to my stomach."
                                                  - C.M. Kornbluth
=======================================================================
                        David J. Schuller
                        modern man in a post-modern world
                        MacCHESS, Cornell University
                        djs63@cornell.edu