Bert, Your self-Patterson peak may be real, i.e. you have pseudo
translation, which can then make the statistics *look* like the crystal
is twinned. Try a self-Patterson (perhaps sharpened) at somewhat lower
resolution, e.g 6 A. Maybe the peak is real, but is only 6% of origin
due to a slight mis-orientation of the molecules. Dave
David Borhani, Ph.D.
D. E. Shaw Research, LLC
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
[email protected]
212-478-0698
http://www.deshawresearch.com <http://www.deshawresearch.com/>
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Van Den Berg, Bert
Sent: Monday, February 16, 2009 9:12 AM
To: [email protected]
Subject: [ccp4bb] Questions about (possibly) twinned data
Hello all,
we have a dataset collected from multiple (2 or 3) parts of the
same crystal with a microbeam (20 micron). The merged data scales OK
(not great) in monoclinic (1-3% rejections). The resolution is 3.2-3.3
A, so the data is not fantastic. This is the cell (similar for other
datasets):
Cell: 70.012 126.449 107.988 90.000 89.946 90.000
p21
Processing in orthorhombic makes the scaling a lot worse, so I'm
assuming its monoclinic for now. Running xtriage gives the following
summary:
------------------------------------------------------------------------
-------
Twinning and intensity statistics summary (acentric data):
Statistics independent of twin laws
- <I^2>/<I>^2 : 1.877
- <F>^2/<F^2> : 0.834
- <|E^2-1|> : 0.663
- <|L|>, <L^2>: 0.411, 0.235
Multivariate Z score L-test: 6.737
The multivariate Z score is a quality measure of the
given
spread in intensities. Good to reasonable data are
expected
to have a Z score lower than 3.5.
Large values can indicate twinning, but small values do
not
necessarily exclude it.
Statistics depending on twin laws
-----------------------------------------------------------------
| Operator | type | R obs. | Britton alpha | H alpha | ML alpha
|
-----------------------------------------------------------------
| h,-k,-l | PM | 0.167 | 0.367 | 0.339 | 0.152
|
-----------------------------------------------------------------
Patterson analyses
- Largest peak height : 5.962
(corresponding p value : 0.72096)
The largest off-origin peak in the Patterson function is 5.96%
of the
height of the origin peak. No significant pseudotranslation is
detected.
So, I'm assuming that these crystals are monoclinic and that
they are pseudo-merohedrally twinned. Is this a reasonable assumption? I
get a decent solution for the P21 data from molecular replacement with a
50% identical model (LLG 900, with the rotation Z-scores low (4-5), but
the corresponding translation Z-scores high (8-20)).
My questions are: what would be the best way to refine? More
specifically, what twin fraction should be used as the different tests
give different fractions. Is the twin fraction automatically determined
in phenix.refine or does this need to be specified? Finally, can
twinning be responsible for the fact that the data do not scale well
(using data collected on different parts of the same crystal)?
Any hints appreciated!
Cheers, Bert
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [email protected]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm
