Dear members,
I am doing a molecular replacement of a transcription factor whose
ligand binding structure(24000 Da) is available in PDB but not for
the DNA binding(13000 Da). When i am searching for the two copies
from ligand binding domain as a template model, i am getting very
good solution but i am not getting any density for the DNA binding
domain to build up in density. The space gorup is P 1 21 1 (4) and
unit cell parameters are Unit Cell: 57.43
69.36 105.99 90.00 90.00
90.00. Please guide me how to get the complete model structure. Table
below show the matthews statistics
For estimated molecular weight 37000.
Nmol/asym
Matthews Coeff %solvent
P(2.20)
P(tot)
_____________________________________________________________
1 5.71
78.46 0.00
0.01
2
2.85
56.91 0.62
0.70
3
1.90
35.37 0.37
0.29
4
1.43
13.82 0.00
0.00
_____________________________________________________________
The
phaser molecular replacement gives the following table.
istogram
of relative frequencies of VM values
----------------------------------------------
Frequency of most common VM value normalized to 1
VM
values plotted in increments of 1/VM (0.02)
<--- relative frequency --->
0.0 0.1 0.2 0.3 0.4 0.5 0.6
0.7 0.8 0.9 1.0
| | | |
| | | |
| | |
10.00 -
8.33 -
7.14 -
6.25 -
5.56 -
5.00 -
4.55 -
4.17 -
3.85 --
3.57 ---
3.33 ------
3.12
----------
2.94 ****************
(COMPOSITION*1)
2.78
-----------------------
2.63
--------------------------------
2.50
-----------------------------------------
2.38
------------------------------------------------
2.27 --------------------------------------------------
2.17 -----------------------------------------------
2.08 --------------------------------------
2.00 --------------------------
1.92
---------------
1.85 -------
1.79 ---
1.72 -
1.67
-
1.61 -
1.56 -
1.52 -
1.47 * (COMPOSITION*2)
1.43 -
1.39 -
1.35 -
1.32 -
1.28 -
1.25
-
TABLE : Cell Content Analysis:
SCATTER
:N*Composition
vs Probability:0|3x0|1:1,2:
$$
N*Composition Probability
$$
loggraph $$
1 0.306066
2 0.00141804
$$
Most probable VM for resolution = 2.27817
Most
probable MW of protein in asu for resolution = 92664.2
I have
initially indexed the data in C2221 but Rfree was not decreasing so i
reindexed the data in data in P121 space group keeping the
Rfree flag of C2221. While analysing the symmetry mates , i found
large space but no density. structure of Ligand binding domain is
almost identical with 90% identity in sequence. I am stuck with this
problem and don't know how to process further.
I run the phenix.xtriage to evaluate the twining but it suggest no twining. When i reindex from C2221 to P21, the completeness of data reduced from 95 % to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2 resolution. I do not understand why the completeness of data reduced so much on reindexing. please Can anyone explain this phenomenon.
Please give me your
valuable suggestion. I will appreciate your effort.
Thank you