Dr.Zwart, Thanks for the reply. 2. The systematic absences and the Rsym support the P3121.I already mentioned the model fit very with the map if I use the P3121. 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the molecules will crash.Besides,the overall FOM ( lower than 0.4) and the R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg. 4. TLS refinement also did not imrove the results. 5. There are totally 88 aa in my protein, I could build 86 aa clearly. The intensity ststistics is attached in the message. J.X. QI ************************************************************************ Shell I/Sigma in resolution shells: Lower Upper % of of reflections with I / Sigma less than limit limit 0 1 2 3 5 10 20 >20 total 50.00 4.95 0.9 1.5 1.9 2.4 2.8 4.0 9.5 90.5 100.0 4.95 3.93 0.0 0.2 0.3 0.5 0.8 2.0 6.6 93.4 100.0 3.93 3.44 0.2 0.3 0.6 1.0 2.5 5.4 15.4 84.6 100.0 3.44 3.12 0.0 0.2 0.5 0.7 2.5 7.6 22.7 77.3 100.0 3.12 2.90 0.3 1.0 2.1 3.2 7.2 17.6 41.4 58.6 100.0 2.90 2.73 0.0 0.7 2.0 3.2 9.9 20.8 52.9 47.1 100.0 2.73 2.59 0.0 1.4 2.9 5.7 12.4 30.0 60.8 39.2 100.0 2.59 2.48 0.7 1.6 4.7 7.7 16.3 36.0 71.5 28.5 100.0 2.48 2.38 0.6 2.1 5.0 10.2 21.9 42.0 76.2 23.8 100.0 2.38 2.30 0.8 2.3 7.4 12.7 25.3 49.4 83.4 16.6 100.0 All hkl 0.4 1.1 2.7 4.7 10.0 21.1 43.4 56.6 100.0 Summary of reflections intensities and R-factors by shells R linear = SUM ( ABS(I - <I>)) / SUM (I) R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) ) In all sums single measurements are excluded Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 4.95 619.8 13.8 3.5 1.039 0.046 0.050 4.95 3.93 834.6 17.5 5.0 1.156 0.048 0.052 3.93 3.44 521.9 14.6 4.5 1.026 0.059 0.062 3.44 3.12 333.7 11.1 4.1 1.073 0.071 0.068 3.12 2.90 172.5 7.1 3.6 1.153 0.098 0.096 2.90 2.73 131.4 6.0 3.4 1.256 0.116 0.108 2.73 2.59 102.8 5.2 3.4 1.306 0.140 0.130 2.59 2.48 77.7 4.6 3.4 1.381 0.173 0.158 2.48 2.38 64.1 4.3 3.3 1.355 0.195 0.177 2.38 2.30 54.7 4.1 3.3 1.345 0.221 0.197 All reflections 297.8 8.9 3.7 1.209 0.071 0.059 Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 2 -0.2 0.4 -0.5 0 0 4 0.1 1.0 0.1 0 0 5 0.4 1.4 0.3 0 0 7 1.1 2.5 0.4 0 0 8 0.4 2.1 0.2 0 0 10 7.3 3.4 2.2 0 0 11 6.0 3.5 1.7 0 0 13 -2.3 4.9 -0.5 0 0 14 6.1 4.3 1.4 0 0 16 8.1 5.1 1.6 0 0 17 3.9 4.9 0.8 0 0 19 0.8 4.5 0.2 0 0 20 4.0 4.6 0.9 ********************************************************************* 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 <jxqi at mail.im.ac.cn>:
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 phenixbb at phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb