[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: 70.012 126.449 107.98890.00089.94690.000 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: bert.vandenb...@umassmed.edu http://www.umassmed.edu/pmm/faculty/vandenberg.cfm
Re: [ccp4bb] Questions about (possibly) twinned data
Hi Bert, It seems unikely you are experiencing merohedral twinning in your crystal since none of your unit cell dimensions are equal length or integer multiples. For your cell, you would expect to see multiple lattices. Is it possible you have a dimer in the asymmetric unit? Strong NCS parallel to a principle lattice direction can sometimes give twin-like statistics especially at lower resolutions. Hope this helps, Chris On Mon, 16 Feb 2009, Van Den Berg, Bert wrote: 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: 70.012 126.449 107.98890.00089.94690.000 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: bert.vandenb...@umassmed.edu http://www.umassmed.edu/pmm/faculty/vandenberg.cfm Christopher L. Colbert, Ph.D. InstructorPhone: (214) 645 5944 University of Texas Southwestern Medical Center FAX: (214) 645 5945 6001 Forest Park Lane Dallas, TX 75390
Re: [ccp4bb] Questions about (possibly) twinned data
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 david.borh...@deshawresearch.com 212-478-0698 http://www.deshawresearch.com http://www.deshawresearch.com/ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Van Den Berg, Bert Sent: Monday, February 16, 2009 9:12 AM To: CCP4BB@JISCMAIL.AC.UK 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: 70.012 126.449 107.98890.00089.94690.000 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: bert.vandenb...@umassmed.edu http://www.umassmed.edu/pmm/faculty/vandenberg.cfm
