[phenixbb] DEN refinement

marinabb phenix marinabb.phenix at gmail.com
Mon Aug 25 01:12:27 PDT 2014

Dear all,

I am trying to use DEN refinement as implemented in the Phenix-1.9 release
to refine a structure at 3.6 Angstrom resolution. The asu consists of 8
copies of hetero-dimers (of roughly 40 KDa sunbunits each). The structure
of one of the subunits has already been solved at about 2 Angstrom, whereas
for the other no homologous model is available. After automatic + manual
building, I have now a model with Rfree = 28 / R = 23, with some protomers
better built than others. I have used this pdb model as input for DEN
refinement, adding the known higher-resolution structure as a (partial)
reference model, and ncs restraints previously found (and run a DEN
parameters optimisation). The final DEN Rfee got significantly worse.

I would appreciate any advise for a better DEN strategy to be adopted in
this case, if possible. In particular I was wondering whether it can be
worth building a model for the missing subunit (or part of it) based on
structural similarity of the current unrefined 3D structure.

I thank you in advance for the suggestions.
With kind regards,

  Marina Mapelli, PhD
  Department of Experimental Oncology
  European Institute of Oncology
  Via Adamello 16, 20139 Milan, Italy
  tel:  +39-02-94375018
  email: marina.mapelli at ieo.eu
  web: http://www.ifom-ieo-campus.it/research/mapelli.php
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