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
