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<p style="margin-bottom:0in">Dear members,
<br><br>
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<br><br>
For estimated molecular weight 37000.<br>Nmol/asym
Matthews Coeff %solvent
P(2.20)
P(tot)<br>_____________________________________________________________<br>
1 5.71
78.46 0.00
0.01<br> 2
2.85
56.91 0.62
0.70<br> 3
1.90
35.37 0.37
0.29<br> 4
1.43
13.82 0.00
0.00<br>_____________________________________________________________<br><br><br>The
phaser molecular replacement gives the following table.<br>istogram
of relative frequencies of VM values<br>
----------------------------------------------<br>
Frequency of most common VM value normalized to 1<br> VM
values plotted in increments of 1/VM (0.02)<br><br>
<--- relative frequency ---><br>
0.0 0.1 0.2 0.3 0.4 0.5 0.6
0.7 0.8 0.9 1.0 <br>
| | | |
| | | |
| | | <br>
10.00 -<br> 8.33 -<br> 7.14 -<br>
6.25 -<br> 5.56 -<br> 5.00 -<br>
4.55 -<br> 4.17 -<br> 3.85 --<br>
3.57 ---<br> 3.33 ------<br> 3.12
----------<br> 2.94 ****************
(COMPOSITION*1)<br> 2.78
-----------------------<br> 2.63
--------------------------------<br> 2.50
-----------------------------------------<br> 2.38
------------------------------------------------<br>
2.27 --------------------------------------------------<br>
2.17 -----------------------------------------------<br>
2.08 --------------------------------------<br>
2.00 --------------------------<br> 1.92
---------------<br> 1.85 -------<br>
1.79 ---<br> 1.72 -<br> 1.67
-<br> 1.61 -<br> 1.56 -<br>
1.52 -<br> 1.47 * (COMPOSITION*2)<br>
1.43 -<br> 1.39 -<br> 1.35 -<br>
1.32 -<br> 1.28 -<br> 1.25
-<br><br>TABLE : Cell Content Analysis:<br>SCATTER <br>:N*Composition
vs Probability:0|3x0|1:1,2: <br>$$<br>N*Composition Probability<br>$$
loggraph $$<br>1 0.306066<br>2 0.00141804<br>$$<br><br>
Most probable VM for resolution = 2.27817<br> Most
probable MW of protein in asu for resolution = 92664.2<br><br>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.<br></p><p style="margin-bottom:0in">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.</p><p style="margin-bottom:0in">Please give me your
valuable suggestion. I will appreciate your effort.<br>Thank you</p>
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