[phenixbb] New UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?
Zhou, Tongqing (NIH/VRC) [E]
tzhou at mail.nih.gov
Mon May 14 12:17:39 PDT 2012
Dear All,
Kay helped me reprocess the data set with XDS, the program pick up I422 as space group. It turned out that when I originally used XDS, I used spindle axis -1, 0, 0 for the APS ID22 detector, it should be 1, 0, 0. The output from XDS:
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
8.87 4414 841 858 98.0% 2.7% 3.2% 4402 45.77 3.0% 99.9* -18 0.664 577
6.33 7883 1374 1385 99.2% 3.7% 3.9% 7872 35.76 4.1% 99.9* -17 0.687 1108
5.18 10205 1724 1734 99.4% 5.1% 4.9% 10195 29.38 5.6% 99.8* -15 0.748 1468
4.49 12194 2042 2055 99.4% 5.0% 4.7% 12185 30.77 5.4% 99.8* -20 0.727 1764
4.02 13830 2284 2297 99.4% 6.2% 5.9% 13822 24.55 6.7% 99.8* -15 0.736 2019
3.67 15377 2501 2530 98.9% 9.4% 9.3% 15368 16.77 10.3% 99.6* -12 0.752 2245
3.40 16709 2702 2724 99.2% 14.3% 14.5% 16700 11.31 15.6% 99.2* -5 0.761 2430
3.18 18091 2904 2934 99.0% 23.3% 24.6% 18084 7.14 25.4% 98.4* -3 0.726 2635
3.00 18105 2972 3107 95.7% 37.3% 40.4% 18071 4.42 40.7% 96.4* -6 0.665 2624
total 116808 19344 19624 98.6% 8.2% 8.4% 116699 18.79 9.0% 99.8* -10 0.724 16870
Attached please also find the xtriage log for data processed with XDS.
Final model with I422 data set at 3 A resolution looked fine to me, r-free went down from ~0.32 to 0.298, the map even let me correctly fitted one place that supposed to have a Cis-Pro. The final numbers for the model is:
r_work = 0.2611
r_free = 0.2983
bonds = 0.002
angles = 0.568
Thank you all for all the help!
Regards,
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4609B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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-----Original Message-----
From: Pavel Afonine [mailto:pafonine at lbl.gov]
Sent: Tuesday, May 08, 2012 2:07 PM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?
Hi,
>> 1. Is it really twinned since including twin-law in refinment gave much
>> better numbers?
R-factors may not be directly comparable:
G.Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261.
The strategy is:
- check to see if Xtriage tells it's twinned (based on reflection statistics, not just predicted twin laws based on geometry);
- use phenix.model_vs_data to see if it's worth using it.
Pavel
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