[sharp-discuss] Extending 3.9A phases to 2.6

[Stefan Arold]

I had recently quite tremendous success in using pirate - instead of 
solomon - after sharp (2.6 A SAD data, only 1 SelMet/300 amino-acids, 
Declerck et al. PNAS 2007). You don't need the solvent content to do that.
In another case (Poncet-Montage et al. JBC 2007), I used dmmulti to 
extend 4.0 MAD (sharp) phases to a 2.3 A native. For the native, phaser 
could place a <15 % homologous structure. However, the structure was so 
different that it could not be refined.  After Dmmulti, phases were 
surprisingly good. In this particular case, MAD and native data looked 
isomorphous, but 'one-crystal' phase extention (dm, resolve) did fail. 
Obviously,  for dmmulti you'd need at least some idea where your protein 
is. But then again, maybe your MAD phases will allow you to define some 
sort of envelope, and transformation is unity (to be refined).

maybe that helps

Cheers
Stefan



Frank von Delft a écrit :

> Hi
>
> I'm sitting with a slightly tricky one here, Se-MAD phases to 3.9, 
> native to 2.6 (peak,remote,native).  HA refinement runs very stably, 
> substructure is complete and all that, now I'm trying to get the 
> phases extended to 2.6A, and wanted to ask if there tips for the best 
> solvent flattening.
>
> 1) Solvent content by matthews should be 76% (enough Se for 1 
> mol/ASU), but I(4) looks better at 50%, as does I(4)/I(1) (which is 
> what solvent optimization uses).  Is this usual?
>
> 2) I don't see too much difference between the two hands, both for 
> I(4) and I4/I1;  does this mean I have not in fact solved the 
> substructure, or just that the phase extension is struggling?
>
> 3) The envelope looks a bit cleaner for P4132 than P4332, but I don't 
> really see protein-like features (the odd sheet or helix would be nice).
> What are the main parameters to play with?  I do a DM run first every 
> time, because the sharp maps don't show much info either.
>
> Any tips would be very useful; I scoured the manual but maybe missed 
> the useful bits.
>
> Cheers
> phx
>
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-- 
==================================================
Stefan T. Arold, PhD
Centre de Biochimie Structurale
CNRS UMR 5048 - UM 1 - INSERM UMR 554
29 rue de Navacelles 34090
MONTPELLIER Cedex  - France
email: Stefan.Arold at cbs.cnrs.fr
Phone: +33 (0)4.67.41.77.02
Fax:   +33 (0)4.67.41.79.13
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