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CCP4BB  November 2010

CCP4BB November 2010

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Subject:

Re: pseudotranslation in C2 space group

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Tue, 9 Nov 2010 10:53:41 +0000

Content-Type:

text/plain

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Parts/Attachments

text/plain (239 lines)

1) Are you sure your  model is only a monomer alone?

2) The first 4 rotation peaks indicate there is probably a trimer, and 
in the same orientation probably as the one in the native. rotation peak 
1 and 2 generate almost the identity matrix.

What are the cells for  the 2 forms?
Eleanor



11/08/2010 12:25 PM, intekhab alam wrote:
> Hi, There
>
> 1.I have collected two data sets one for the native protein (60Kda) and
> complex of native with other protein of 8 Kda. The shape of native dataset
> is cubic while that of the complexed one is triangular. A number of dataset
> were collected for these two and i successfully indexed them to a spacegroup
> of C2.
>
> 2.While doing molecular replacement  for the native data using a monomeric
> template clear solution with 3 monomers in the asyymetric unit was obtained
> and structure solved successfully with R/rfee of 19/23 at 2.5A reolution.
>
> 3.The molecular replacement of the complexed dataset with the same template
> gave a solution with 2 monomers in asymmetric unit with a lot of clashes
> between the two subnuints. when i closely examined the logfile i observed
> that there was pseudotranslation detected by the program in all of  my
> complex dataset. I run xtiage as well as pointless and truncate which rules
> out any twinning as well as wrong space group assignment. Pseudotranslation
> of 18% has been detected by balbes.
>
> 4. I also run the Balbes at Murshodov server which gave a solution with 4
> monomers in the asymmetric but still showing a lot of clashes in the
> asymmetric unit  (R/Rfree 0.43/0.47)  followed by automatic refinemnet with
> Arp/wARp which gave a model . When i examine the density of the model i saw
> a lot of clashes in the asymmetric unit but the density are interpretable so
> that bakbone can be easily modelled. But the R and R free donot goes down
> from (R/Rfree 0.43/0.47)
>
> I have pasted the logfile below from molrep for your convenience. Kindly
> suggest me how can i proceed with this dataset. That will be very kind of
> you if you spend some time over my problem.  Another question , is it
> possible that this pseudotranslation is due to the smaller protein of the
> complex which has slightly changed the crystal packing. ( SDS done on  the
> complex  crystals clearly showed the presence of both the proteins).
>
>
>
>
>   --- Check Patterson for pseudo-translation ---
>     PST_limit :   0.125 of origin peak
>   INFO: pseudo-translation was detected.
>          Origin Patterson peak: P,P/sig :     80563.180       266.237
>          1 Patterson. peak    : p,P/sig :     80560.719       266.228
>          2 Patterson peak     : P,P/sig :     13992.708        46.242
>          3 Patterson peak     : P,P/sig :     13992.708        46.242
>          Peak 1: trans.vector /ort/ :        60.164        98.423
> 0.000
>                  trans.vector /frac/:         0.500         0.500
> 0.000
>          Peak 2: trans.vector /ort/ :        31.861         0.000
> 0.000
>                  trans.vector /frac/:         0.265         0.000
> 0.000
>          Peak 3: trans.vector /ort/ :        28.303        98.423
> 0.000
>                  trans.vector /frac/:         0.235         0.500
> 0.000
>   INFO:  translation vector of peak 2 will be used.
>   WARNING: with keyword: PST -->  MODE = F , STICK = N
>
>   Sol_ Space group : C 1 2 1
>   Sol_ No:   5 Sett:   2
>   Sol_ Cell: 120.328 196.846 109.285   90.00  113.84   90.00
>
>   Sol_--- Rotation function ---
>   Sol_
>    Radius of gyration          :   23.58
>   Sol_ Radius of integration   :   47.16
>   Sol_ Resmin,Resmax           :   48.03    2.42
>    WARNING: For this radius integration program uses data included
>             between    48.0 and    2.71 (angstrom..)
>   --- rfcoef for model ---
>   --- rfcoef for Fobs ---
>    NCS (from Self rotation Function):     1
>    NCS_model (from Model Self rotation Function):     1
>    Program will use NCS_model =:     1
>
>    Number of RF peaks :      30
>               theta    phi     chi    alpha    beta   gamma      Rf
> Rf/sigma
>   Sol_RF   1   106.45   50.40    1.37  320.21    1.31   39.41    0.9325E+05
> 19.98
>   Sol_RF   2     0.00    0.00    0.00    0.00    0.00    0.00    0.8668E+05
> 18.57
>   Sol_RF   3   158.10   -1.79  120.96  209.61   37.87   33.18    0.8147E+05
> 17.46
>   Sol_RF   4    22.21 -179.07  120.40  149.19   38.30  327.33    0.7596E+05
> 16.28
>   Sol_RF   5     0.83  144.00  179.87  143.94    1.66   35.93    0.4234E+05
> 9.07
>   Sol_RF   6   146.73   90.95   73.37  329.03   38.27  327.14    0.3574E+05
> 7.66
>   Sol_RF   7     0.00    0.00  179.92   97.16    0.00   82.76    0.3504E+05
> 7.51
>   Sol_RF   8    34.01   88.19   71.45   29.00   38.12   32.61    0.3354E+05
> 7.19
>   Sol_RF   9    77.12  174.71   90.84   97.45   87.95  288.04    0.2136E+05
> 4.58
>   Sol_RF  10   134.42  132.29    7.11   39.81    5.07  315.22    0.2089E+05
> 4.48
>   Sol_RF  11   152.93  177.57  136.00   21.98   49.92  206.84    0.1861E+05
> 3.99
>   Sol_RF  12   156.31 -169.21   19.45   91.88    7.78  250.29    0.1849E+05
> 3.96
>   Sol_RF  13   130.28  116.07   92.63  351.98   66.96  299.83    0.1810E+05
> 3.88
>   Sol_RF  14     0.00    0.00   11.30   11.30    0.00    0.00    0.1808E+05
> 3.87
>   Sol_RF  15    36.79  -89.11   90.53  219.84   50.36  218.06    0.1801E+05
> 3.86
>   Sol_RF  16   134.90 -102.85  173.11   82.03   90.00  107.72    0.1761E+05
> 3.77
>   Sol_RF  17   106.06    0.94   54.00  262.92   51.73   81.03    0.1753E+05
> 3.76
>   Sol_RF  18   135.11   85.04  162.00  277.64   88.39  287.56    0.1728E+05
> 3.70
>   Sol_RF  19   127.04  109.26   97.92  344.58   74.03  306.06    0.1722E+05
> 3.69
>   Sol_RF  20   141.26 -144.07   13.23  120.76    8.27  228.90    0.1705E+05
> 3.65
>   Sol_RF  21   142.16 -164.54  114.88   54.42   62.26  203.50    0.1675E+05
> 3.59
>   Sol_RF  22   137.57 -150.27   12.10  115.26    8.16  235.79    0.1657E+05
> 3.55
>   Sol_RF  23   162.01  178.37  129.40   24.79   32.42  208.06    0.1654E+05
> 3.54
>   Sol_RF  24   135.22   28.82   14.02  293.83    9.86   56.20    0.1636E+05
> 3.51
>   Sol_RF  25   134.21   84.96  161.20  278.32   90.00  288.40    0.1621E+05
> 3.47
>   Sol_RF  26    43.85   57.57   90.92    3.81   59.17   68.66    0.1616E+05
> 3.46
>   Sol_RF  27    22.55  173.85  110.70  137.04   36.79  329.34    0.1615E+05
> 3.46
>   Sol_RF  28   142.62   94.57   75.18  333.11   43.47  323.97    0.1612E+05
> 3.46
>   Sol_RF  29    25.92  179.07  113.06  142.75   42.77  324.61    0.1609E+05
> 3.45
>   Sol_RF  30   128.76 -103.39   65.70  144.60   50.05  171.38    0.1599E+05
> 3.43
>    Final number of peaks :      30
>   INFO:    Relations between peaks see in molrep.doc
>    Time:    22h 12m  3s Elapsed:     0h  3m 46s
>   Sol_
>   Sol_--- Translation function ---
>   Sol_ Resmin,Resmax           :   48.03    2.42
>   Sol_ NCS model               :    1
>   --- List of psewdo-translation vectors ---
>   PST_vector  1:   0.265   0.000   0.000
>   ---
>
>    Time_elapsed:     0h  4m  1s Remained:     0h  7m 15s
>   Sol_ RF TF   Tf/sig  TFcntrst  PFind  PF    PFmin  wRfac Scor Scor_max
> Cntrst
>   Sol___1__1   24.83     10.203   1.00  1.00  -4.18  0.595  0.390  0.390
> 0.00
>   Sol___2__1   21.58     11.436   1.00  1.00  -4.13  0.601  0.377  0.390
> 0.00
>   Sol___3_14   4.093      4.995   1.00  1.00  -3.57  0.614  0.353  0.390
> 0.00
>   Sol___4__1   21.04     13.251   1.00  0.98  -3.46  0.607  0.361  0.390
> 0.00
>   Sol___5__1   14.68      3.760   1.00  1.00  -3.25  0.614  0.349  0.390
> 3.99
>   Sol___6__6   5.017      0.269   1.00  1.00  -4.19  0.625  0.325  0.390
> 3.14
>   Sol___7__1   13.18      3.772   1.00  1.00  -3.18  0.617  0.342  0.390
> 3.14
>   Sol___8__6   4.372      2.119   1.00  1.00  -3.86  0.622  0.332  0.390
> 3.02
>   Sol___9__3   4.122      2.055   1.00  1.00  -3.41  0.626  0.318  0.390
> 3.20
>   Sol__10__2   4.511      1.500   1.00  1.00  -3.91  0.627  0.317  0.390
> 2.96
>   Sol__11__2   4.970      2.936   1.00  1.00  -3.99  0.628  0.316  0.390
> 2.79
>   Sol__12__5   3.856      1.531   1.00  1.00  -3.73  0.628  0.313  0.390
> 3.01
>   Sol__13__6   3.437      1.204   1.00  1.00  -4.07  0.629  0.315  0.390
> 2.92
>   INFO: contrast is good enough. Stop this run
>
>    --- Summary ---
>
>   S_ RF TF       theta    phi     chi    tx     ty     tz    TFcnt wRfac
> Scor
>
>   S___1__1   1  106.45   50.40    1.37  0.352  0.000  0.273  10.20  0.595
> 0.390
>   S___2__1   2    0.00    0.00    0.00  0.352  0.000  0.273  11.44  0.601
> 0.377
>   S___4__1   3   22.21 -179.07  120.40  0.104  0.000  0.167  13.25  0.607
> 0.361
>   S___3_14   4  158.10   -1.79  120.96  0.489  0.000  0.386   5.00  0.614
> 0.353
>   S___5__1   5    0.83  144.00  179.87  0.216  0.000  0.272   3.76  0.614
> 0.349
>   S___7__1   6    0.00    0.00  179.92  0.216  0.000  0.272   3.77  0.617
> 0.342
>   S___8__6   7   34.01   88.19   71.45  0.178  0.000  0.186   2.12  0.622
> 0.332
>   S___6__6   8  146.73   90.95   73.37  0.368  0.000  0.225   0.27  0.625
> 0.325
>   S___9__3   9   77.12  174.71   90.84  0.482  0.000  0.245   2.06  0.626
> 0.318
>   S__10__2  10  134.42  132.29    7.11  0.075  0.000  0.233   1.50  0.627
> 0.317
>   S__11__2  11  152.93  177.57  136.00  0.091  0.000  0.216   2.94  0.628
> 0.316
>   S__13__6  12  130.28  116.07   92.63  0.473  0.000  0.197   1.20  0.629
> 0.315
>   S__12__5  13  156.31 -169.21   19.45  0.084  0.000  0.319   1.53  0.628
> 0.313
>
>   Contrast =     2.92
>
>   Sol_
>   S_ Nmon RF TF   theta    phi    chi     tx     ty     tz    TFcnt  wRfac
> Scor
>   S__ 2   1   1  106.45   50.40    1.37  0.352  0.000  0.273  10.20  0.595
> 0.390
>
>
> PST_vector was used  1:   0.265   0.000   0.000
>   --- convert "molrep.crd" to "molrep.pdb" ---
>

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