[sharp-discuss] K2PtI6 cluster

[gb10@globalphasing.com]

Dear Robbie,

     I guess this compound must be below the limit of what one would call a 
cluster, as it has only one metal atom. Usually we use the name 'cluster' 
for compounds such as Ta6Br12++ or the phosphotungstates containing 12 or 18 
tungstens, or another 4-mercury compound whose initials elude me just now 
(TAMM?). A characteristic of these clusters is that they often bind in rather 
ill-defined orientations, so that their contribution to the diffraction 
pattern is best represented as that of their spherical average in the first 
instance. The old (1.4.0) version of SHARP provides this facility for experts, 
in a way which Clemens Vonrhein can tell you more about (it was used in the 
phasing of the 30S ribosomal subunit). 

     In the case of PtI6--, however, there is only one metal atom, and it 
will usually be coordinated directly to the protein through the replacement 
of one of the iodines by a sulfur atom from Cys or Met, or by the imidazole 
group of a His. There is therefore no need to use a cluster model. 

     I would recommend that you start off by using a single Pt atom at each 
main position corresponding to those given by your solution of the Patterson, 
with a 'reasonable' B factor which would be roughly the B factor of your data 
(I know that this is not so easily estimated at 3.3 Angstroms, but this should 
soon be made easier by some 'intelligent scaling' which we are about to put 
into SHARP). After refining this model to convergence, look at the residual 
maps - both isomorphous and anomalous - around the Pt site, and see whether 
there are features indicating the position of iodine atoms around it. 

     At what wavelength were your data recorded? With CuKalpha, you should 
see quite a lot of anomalous signal coming from the iodines.

     Please let us know if you encounter any difficulties in following this 
procedure. Looking at residual maps is perhaps the most important part of 
using SHARP, so make sure that you have the graphical helper application 
hooked in properly (if not, ask for help).


     With best wishes,

          Gerard.

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     * Gerard Bricogne                     gb10@GlobalPhasing.com  *
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--
Original message from firstname lastname:
> 
> Hi all,
> I have found a K2PtI6 cluster by patterson methods.  The problem is that the 
> data only extends to 3.3 angstroms and this is not good enough to distinguish, 
> refine and phase with the Iodines.  I want to do SIRAS as I have a native data 
> set and there is a detectable bijvoet difference.  Any suggestions?  thanks in 
> advance.
> Robbie Reutzel
> Center for Structural Biology
> University of Florida
> -------------------
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