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
>
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>
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>
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>
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