Self rotation is not very clear - and the top peaks are almost certainly 
generated partly by the high crystallographic symmmetry.

 Things to check:
1) native Patterson - is there a non-crystallographic translation? 
ctruncate checks this for you.

2) twinning - if there is a non-crystallographic translation many of the 
twinning tests are somewhat invalidated. again I have found the Ltest 
which is now incorporated into ctruncate and only applied to reliable 
data is quite informative. Probably phenix.xtriage has looked for this 
but you should check the loggraphs too.

PG 622 can be twinned in several ways ( see $CHTML/winned info)

3) Only the old self rotation programs show you all symmetry equivalents 
of your peaks - I cant work out in my head whether any of the ones you 
list indicate NCS 3-folds..

But I would expect to find a solution with the larger protein with 100% 
sequence ID. Maybe try searching at low resolution with the whole 
molecule instead of splitting it into domains?
Eleanor


 


 



Wei Zhang wrote:
> Dears,
> I am doing molecular replacement of a protein complex with a P622 data set
> with large cell parameters (a=b=135, c=480). The data set seems well. R
> merge is 0.17 for all and 0.70 for the last shell of 2.9 angstrom. I am not
> sure it is a complex in the crystal. Phenix analysis reveal there is no
> twin. The proposed protein complex is about 70 kDa with a larger subunit of
> 50 kDa and a small subunit of 20 kDa. The matthews analysis indicates that
> there might be 3 complexes in the ASU. The structure of the 50 kDa subunit
> is known while the 20 kDa one is unknown. But molecular replacement failed
> with either Phaser or Molrep.
> Self-rotation with CNS reported the result as below:
>  ! index, psi, phi, kappa, RF-function ( 0.25)
>  1     0.000   0.000 180.000   29.7217
> Self-ratation with Molrep reported the result as below:
>   Number of RF peaks :      30
>              theta    phi     chi    alpha    beta   gamma      Rf
> Rf/sigma
>  Sol_RF   1     0.00    0.00    0.00    0.00    0.00    0.00    0.3444E+05
> 17.13
>  Sol_RF   2    90.00  -80.07  179.99    0.00  180.00  -19.86     5061.
> 2.52
>  Sol_RF   3    90.00  -65.53  179.99    0.00  180.00  -48.94     4890.
> 2.43
>  Sol_RF   4    90.00  -76.12  179.99    0.00  180.00  -27.76     4722.
> 2.35
>  Sol_RF   5    11.42   90.00   61.00   30.00   11.53   30.00     2438.
> 1.21
>  Sol_RF   6   164.38   60.00  179.99   60.00  -31.24  120.00     1850.
> 0.92
>  Sol_RF   7    85.13 -141.54  179.97   38.32 -170.26  141.40     1805.
> 0.90
>  Sol_RF   8    90.00  -60.00   90.00   30.00  -90.00  -30.00     1764.
> 0.88
>  Sol_RF   9    84.07 -144.87  179.96   34.98 -168.15  144.73     1743.
> 0.87
>  Sol_RF  10    72.25  -60.00   89.30   46.76  -84.03  -13.24     1665.
> 0.83
>  Sol_RF  11   138.24 -130.77  180.00   49.23   83.52  130.77     1608.
> 0.80
>  Sol_RF  12   170.36   30.00  179.99   30.00  -19.28  150.00     1590.
> 0.79
>  Sol_RF  13    82.04   60.00  179.99   60.00 -164.07  120.00     1571.
> 0.78
>  Sol_RF  14   141.01   30.00  179.99   30.00  -77.99  150.00     1554.
> 0.77
>  Sol_RF  15   123.63 -155.38  179.98   24.62  112.74  155.38     1517.
> 0.75
>  Sol_RF  16   148.80   30.00  179.99   30.00  -62.39  150.00     1450.
> 0.72
>  Sol_RF  17   142.61   30.00  180.00   30.00  -74.78  150.00     1439.
> 0.72
>  Sol_RF  18    72.25 -150.00  179.99   30.00 -144.50  150.00     1422.
> 0.71
>  Sol_RF  19    47.42 -120.00  179.98   60.00  -94.83  120.00     1417.
> 0.71
>  Sol_RF  20   153.12   30.00  179.98   30.00  -53.75  150.00     1292.
> 0.64
>  Sol_RF  21   155.99   30.00  179.98   30.00  -48.01  150.00     1274.
> 0.63
>  Sol_RF  22   138.05   30.00  179.99   30.00  -83.91  150.00     1258.
> 0.63
>  Sol_RF  23    54.12  120.00   89.15   60.00   69.32    0.00     1254.
> 0.62
>  Sol_RF  24   129.04 -136.48  179.99   43.52  101.93  136.48     1193.
> 0.59
>  Sol_RF  25   138.65 -164.29  179.99   15.71   82.69  164.29     1185.
> 0.59
>  Sol_RF  26    84.16   51.37  179.98   51.37 -168.32  128.63     1176.
> 0.59
>  Sol_RF  27    90.00  150.00   59.82   60.00   59.82  -60.00     1162.
> 0.58
>  Sol_RF  28    43.66 -133.74  179.98   46.26  -87.31  133.74     1161.
> 0.58
>  Sol_RF  29   127.85 -169.33  179.99   10.67  104.29  169.33     1153.
> 0.57
>  Sol_RF  30   124.15   30.00  179.99   30.00 -111.71  150.00     1147.
> 0.57
>
> My question is:
> 1. For a 70 kDa protein compelx, is it common to have such a large cell with
> a dimention as long as 480 angstrom?
> 2. Is it possible that the longest dimention of cell is doubled? If it is,
> how to divide it?
> 3. How to interpret the self-rotation results. The results from CNS and
> Molrep differs so much.
> 4. Any other suggestions on the molecular replacement are appraciated.
>
> Thanks.
>
> Wei Zhang
> PKU
>
>