From: Jon Schuermann
Date: 10 October 2011 22:41
I am sure this has happened many many times before but I cannot find a reference. I have a protein/DNA complex structure where the protein has P212121 symmetry, but the DNA only has P21 symmetry. I know its pseudosymmetry caused by the NCS. Has anyone seen this with protein/DNA or have a reference I can add to my paper?
Thanks so much,
Jon
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
----------
From: James Holton
I think this is called "P21", with the additional annoyance that you
need to pick your Rfree set in P212121 and then symmetry-expand it.
Otherwise, your NCS operators will constrain your "free" reflections
to have the same intensity as their "NCS mates". I'm sure you didn't
make that mistake, but a lot of other people have.
I suppose you could still call this "NCS", for "nearly
crystallographic symmetry". But I think the general term
"pseudosymmetry" is what I would use in a paper.
I have seen one case (1FYK) where the protein followed the cannonical
crystallographic symmetry and the DNA was disordered along the screw
of the double helix. Since O.L. was having a hard time interpreting
the DNA density, he re-grew the crystals with a new oligo containing a
single iodinated base to try and clear up the register, only to find
that the iodine difference map lit up _every_ base in the DNA ladder,
forming a beautiful double helix, with one atom! That is: all the
"base pairs" in the density was actually composed of an equal portion
of all the bases in the oligo.
Not exactly the situation you are in, but definitely a case where one
part of the ASU had different "symmetry" than another.
-James Holton
MAD Scientist
Date: 10 October 2011 22:41
I am sure this has happened many many times before but I cannot find a reference. I have a protein/DNA complex structure where the protein has P212121 symmetry, but the DNA only has P21 symmetry. I know its pseudosymmetry caused by the NCS. Has anyone seen this with protein/DNA or have a reference I can add to my paper?
Thanks so much,
Jon
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
----------
From: James Holton
I think this is called "P21", with the additional annoyance that you
need to pick your Rfree set in P212121 and then symmetry-expand it.
Otherwise, your NCS operators will constrain your "free" reflections
to have the same intensity as their "NCS mates". I'm sure you didn't
make that mistake, but a lot of other people have.
I suppose you could still call this "NCS", for "nearly
crystallographic symmetry". But I think the general term
"pseudosymmetry" is what I would use in a paper.
I have seen one case (1FYK) where the protein followed the cannonical
crystallographic symmetry and the DNA was disordered along the screw
of the double helix. Since O.L. was having a hard time interpreting
the DNA density, he re-grew the crystals with a new oligo containing a
single iodinated base to try and clear up the register, only to find
that the iodine difference map lit up _every_ base in the DNA ladder,
forming a beautiful double helix, with one atom! That is: all the
"base pairs" in the density was actually composed of an equal portion
of all the bases in the oligo.
Not exactly the situation you are in, but definitely a case where one
part of the ASU had different "symmetry" than another.
-James Holton
MAD Scientist
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