[phenixbb] low-resolution refinement

Jennifer Weinreich jenn.a.weinreich at gmail.com
Fri Jun 10 17:43:04 PDT 2011


I am refining a low-resolution structure of a protein complex (4.4 Å).
The structure was solved by molecular replacement using structures of
individual subunits as search models.  Here are some of the questions that I
have (and also points raised by our reviewers.)    Your thoughts and
suggestions on how to proceed with this will be very much appreciated.

1) The B factors are very high (300-400).  The Wilson B calculated by
phenix.xtriage is ~200.   Is this something I should be concerned about?

2) What is the expected (or 'acceptable') gap between R and Rfree at this
resolution.  (Current R = 27%, Rfree = 33%)  Does this sound reasonable?

3) It has been suggested to me that I should try adding riding hydrogens
during the last round of refinement (to help with geometry).  Is this
something I should do?
And if so, should I remove them when I deposit the file to the PDB.
(Hydrogens at 4.5A are probably going to raise a lot of eyebrows...

4) What is the 'acceptable' coordinate and phase errors for structures at
this resolution.  (They are now 1.4Å and 36˚)

5) I have been using secondary structure restraints during the refinement,
which seems to work reasonably well.  I also tried refinement using
reference model (the structure of the individual components).  But refining
with reference models seems to result in high RMSD bonds/angles.  Is there
something I'm missing?

Short of growing better crystals, are there other strategies I should be
trying with the existing data?

Thank you!

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