[phenixbb] molecular replacemnt problem

24 Mar 2013

      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

[phenixbb] molecular replacemnt problem

Appu kumar