It seems very likely your crystal is twinned - the moments and
cumulative intensity are a good indicator of twinning, especially when
there isnt much NCS.
But your solution is almost certainly partially correct - the Rfactor is
pretty low.
It is a good idea to run pointless which gives you the correlation
Coefficient for each symmetry operator. see if there is any difference
between the different ones.)
You could have twinning with either 4-fold or 222 symmetry.
the 222 is less likely seeing that would mean the a=b axes are
accidently equal.
If you decide the symmetry is really PG 4 you need to remerge the data
in that point group ( no need to reintegrate - the cell dimensions will
still be the same)
The most likely solution is that one of your P43212 molecules is
corrrect, but it is probably a good idea to run the MR search again.
Use your refined antibody molecule as the search model to save work later..
Eleanor
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
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