Dear Appu,
I am not sure that I have a complete
sense of the issue at hand since some of the
information needed to think your issue
through is missing in your email. For
example, to what high resolution cut-off
were the data measured? What resolution
limits were used for the MR search? How do
the unit cell dimensions and space group in
the two cases compare?
I am guessing the ligand binding domain
in your protein has the identical sequence
to that of the published ligand binding
domain that you use as a template in your MR
search. In any case, here are a couple of my
thoughts:
(1) It might be worth setting up
different runs of MR with different numbers
for expected copies (not just two copies but
also one copy and three copies just in case
you have one of the extreme cases of solvent
content)?
(2) If the MR solution is correct and
there is physical room for a DNA binding
domain in your lattice (check by displaying
symmetry mates), perhaps the DNA binding
domain is disordered. In that case (and if
all attempts with current data fail), you
may have to crystallize the protein in
presence of DNA.
Good luck!
Raji
On Sat, Mar 23,
2013 at 2:26 PM, Appu kumar
<[log in to unmask]>
wrote:
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
Thank a lot in advance
--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical
School
Research Associate, Brigham and Women's
Hospital
Visiting Research Scholar, Brandeis
University
