Just to add another point to look at. If there's any question about the
absences on the 4-fold, e.g. that it could be P4(2)2(1)2, then the real
space group could be P212121.
I mention this because I discussed a structure on here a while ago which
was apparently P42212, would only solve by MR in P41212 (I won't explain
why I even tried that ...) but didn't refine to well and turned out to
be twinned P212121.
This has absences on all 3 axes, but the 4-fold must be 4(2).
Cheers,
Charlie
Matthew Franklin wrote:
Hi all -
I'm trying to solve the structure of an antibody-receptor complex, and I've hit
a wall which may be due to a twinned crystal form. This crystal has the
apparent space group P43212, with cell constants a=64.02 c=274.83. Solvent
content analysis using this space group suggests 1 mol/asu, with 47% solvent,
which would be fairly consistent with the diffraction limit of about 2.8 A.
I've been able to place the antibody using molecular replacement and refine it
to R=0.289, Rf=0.338. There is some density for the receptor, which represents
about 20% of the mass of the complex, but not clear enough to build into, and
all efforts to improve the density or place the receptor by molecular
replacement have failed.
Well, tough luck, you might say, but I noticed at the very beginning of the process that this
crystal form may be a perfect twin. The "4th moment of E" graph from Truncate shows
nearly all resolution bins with values of 1.4 - 1.6, except in the very topmost few bins where the
values rise up to 2. The other moment graphs are likewise at their "perfect twin" values
across the resolution range. The cumulative intensity distribution graph shows the observed values
are about 30% lower than the expected values for both acentric and centric reflections. As I
understand it, both of these are strong indicators of twinning, and the twin fraction analysis in
DETWIN suggests a twin fraction of ~0.5.
So what do I do now? I think I'm supposed to reprocess the data in the space
group without the twin transformation (which would be P43), then run molecular
replacement which should show me solutions for both halves of the twin.
However, all I'm seeing is two copies of the antibody in the (P43) asymmetric
unit, which don't overlap, and both of which need to be present in the same
unit cell in order to form a 3-dimensional lattice. This is exactly what I
would expect to see if there were no twinning present.
So my question is, is this crystal form twinned or not? Is there some way that
the intensity statistics could be misleading me? On the other side, am I doing
something wrong with the structure determination if the crystal is twinned?
How should I proceed?
Thanks for any help anyone can provide.
- Matt
--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems,
a wholly owned subsidiary of Eli Lilly & Company
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116 fax:(212)645-2054
Confidentiality Note:
This e-mail, and any attachment to it, contains privileged and confidential
information intended only for the use of the individual(s) or entity named on
the e-mail. If the reader of this e-mail is not the intended recipient, or the
employee or agent responsible for delivering it to the intended recipient, you
are hereby notified that reading it is strictly prohibited. If you have
received this e-mail in error, please immediately return it to the sender and
delete it from your system.
Thank you.
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[email protected]
+61 8 6488 4406
