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:
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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
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| 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
