[phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold!

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Aug 3 21:23:23 PDT 2010

Hi Joe,

> Thanks so much Pavel for the very rapid response! One more thing, it
> is a disulfide linked DTT so do I do anything special to ensure that
> all the sulfur atoms (4 in total - two in one unit cell - one each
> from the cys and dtt and two in the other unit cell) stay in close
> enough contact for a covalent bond and not move due to non-bonded
> contact distance restraints?

phenix.refine shows a summary of the disulfides like this:

  Number of disulfides: simple=1, symmetry=1
    Simple disulfide: pdb=" SG  CYS A   2 " - pdb=" SG  CYS A  14 " distance=2.09
    Symmetry disulfide: pdb=" SG BCYS A 133 " - pdb=" SG BCYS A 133 " distance=2.12 -x,y,-z

The program should find all disulfides automatically, using the
disulfide_distance_cutoff=3 parameter.
Let us know if the output doesn't look right.


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