[phenixbb] merohedral twinned refinement

Peter Zwart phzwart at gmail.com
Mon Jan 18 08:16:34 PST 2010


>
> 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.

try P31 or otherwise P1. You should get a solution in those groups.

It could of course mean that there are OD type issues, but I would not
jump there yet.

Can you send the intensity statistics from xtriage?

P

>
> 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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>



-- 
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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
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