Bulk solvent scaling & unstructured protein
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! Rgds., Mads ------------------------------ Mads Beich-Frandsen Department of Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria E-mail: [email protected] Phone: +43-1-4277-52225 Fax: +43-1-4277-9522 Web: http://www.mfpl.ac.at/index.php?cid=58
Hi Mads,
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.
yes, with some (slightly tedious) manual work -:) Fill the area where you expect the protein to be with dummy atoms (say water). Make sure that: 1) all DA have zero occupancy so they don't contribute to the scattering; 2) tell phenix.refine to include zero occupancy atoms into mask calculation: "refinement.mask.ignore_zero_occupancy_atoms=False", so the bulk solvent does not enter that area. Let me know if you have questions. Pavel.
participants (2)
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Mads Beich-Frandsen
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Pavel Afonine