[phenixbb] Bulk solvent scaling & unstructured protein

Mads Beich-Frandsen mads.beich-frandsen at univie.ac.at
Wed Mar 24 03:32:37 PDT 2010

Hi all,

I have a P1-crystal and data (quite anisotropic to 2.85Å, 90% complete) of a partly unstructured protein, of which some 35% of the sequence is intrinsically unstructured.
The structure has been solved by molecular replacement, and it has been refined to Rw/Rf 20/26 with Phenix.
As expected, not much of the predicted unstructured region show clear density.

The oligomeric protein packs in layers facing oneanother, leaving the unstructured parts 'packing' towards eachother, in what appears as huge solvent-channels.

My question is now: Is there an approach to optimizing bulk solvent scaling in Phenix, keeping with the thought, that 30-35% of my protein sequence should be present where Phenix assigns bulk solvent.

Thank you!
-And any other tricks and tips will much appreciated!


Mads Beich-Frandsen

Department of Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna

E-mail: mads.beich-frandsen at univie.ac.at
Phone: +43-1-4277-52225
Fax: +43-1-4277-9522
Web: http://www.mfpl.ac.at/index.php?cid=58

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