Dear Gabriel -
You don't say if the two crystals are essentially identical - do they
have the same unit cell parameters? I would imagine so.
The phenomenon you describe is very common with molecular replacement
(is this how you solved it?) or with auto-tracing. Your two structures
are, in fact, identical within the limits of error of the refinement -
this is why they give the same R values. There is no crystallographic
difference between monomer A and monomer A' which is related by a
crystal symmetry transformation. Either one (but not both!) can be
included in the asymmetric unit, but we generally pick a set of monomers
that gives a compact, pleasing arrangement.
I expect that both of your arrangements can be reorganized to give two
complete tetramers, by taking the "orphan" monomers and applying crystal
symmetry transformations (simple unit cell translations, for P1) to
place them in the equivalent position that completes the desired
tetramer. Coot (and most other graphics programs) will generate the
symmetry-equivalent molecules for you and allow you to save them, then
you can just extract chain A (for example) from one PDB file, and paste
it into the other PDB file in place of the chain A that's already there.
Feel free to contact me if that explanation wasn't clear.
- Matt
On 1/22/14 3:50 PM, Gabriel Moreno wrote:
Dear CCP4 Contributors,
I have a bit of a mystery:
Two co-crystals that I picked up from the same grid tray (the two
conditions vary slightly in %PEG and [salt], both indexed as P1 (apo
structure normally crystallizes in P3221). One dataset was indexed,
integrated and scaled with HKL2000. The other was processed with
MOSFILM (could not process in HKL2000). Downstream processing for both
sets was done exactly the same in PHENIX. Though both asymmetric units
contain two complete tetramers, the interesting thing is that the
configuration of monomers is different between the solutions. One
contains one complete tetramer, one trimer (with a void where the
fourth monomer would be), and one monomer on off on its own. The
asymmetric unit of the other dataset solution also contains a complete
tetramer, but then has two dimers. Close analysis of contacts between
symmetrically related molecules reveals that the crystal packing is
exactly the same between the two solutions from the two datasets.
Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other
quality indices are also comparable between the two sets.
Here's my question: Does this phenomenon reveal anything important, or
is this type of thing just seen sometimes with P1 solutions from
crystals of the same protein and condition (more or less).
I hope I have been clear.
Thanks!
Gabriel
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
