[phenixbb] merohedral twinned refinement
JXQI
jxqi at mail.im.ac.cn
Mon Jan 18 04:00:33 PST 2010
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
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