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 <appu.kum...@gmail.com> 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
