merohedral twinned refinement
Dear all, I have a 2.3A data set processed with HKL2000. The space group is P3121 with 63% of solvent content and 1 molecule in the ASU. I used a 40% homology model to do molecular replacement. Both the Phaser and Molrep gave similar solution with good packing. After further refinement with phenix, the built model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to 0.34/0.38. I rechedked the data set with xtriage and found the data set is merohedral twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). When I used the twin law in further refinement, the R/Rfree were only decreased to 0.32/0.36. Any suggestions are appreciated, thanks! J.X. QI
1. How do the intensity statistic look like?
2. How did you choose P3121?
3. Did you try solving and refining in P3?
4. TLS?
5. How complete is your model
2010/1/17 JXQI
Dear all,
I have a 2.3A data set processed with HKL2000. The space group is P3121 with 63% of solvent content and 1 molecule in the ASU. I used a 40% homology model to do molecular replacement. Both the Phaser and Molrep gave similar solution with good packing. After further refinement with phenix, the built model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to 0.34/0.38.
I rechedked the data set with xtriage and found the data set is merohedral twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). When I used the twin law in further refinement, the R/Rfree were only decreased to 0.32/0.36. Any suggestions are appreciated, thanks!
J.X. QI _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------
i have a multi domain protein data of 3.28 A resolution the completness is 92 % it is a 68 KDa protein 3 domains individually i used in phaser and i got the solution but with 4th domain when i am running phaser solution i am getting but the density is not so clear for that . is this due to 92 % completness of data. without 4th domain the R factor and R fre e is 29 / 40
participants (3)
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JXQI
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Peter Zwart
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v_kukshal@cdri.res.in