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. Thank you
On 24 March 2013 13:30, Matthias Zebisch < matthias.zebi...@bbz.uni-leipzig.de> wrote: > the p21 c2221 ambivalence can mean severe twinning (i had a similar case > just now - try several crystals from the same condition) ! > What do the twinning statistics suggest? > > cheers, Matthias > > ----------------------------------------- > Dr. Matthias Zebisch > Division of Structural Biology, > Wellcome Trust Centre for Human Genetics, > University of Oxford, > Roosevelt Drive, > Oxford OX3 7BN, UK > > Phone (+44) 1865 287549; > Fax (+44) 1865 287547 > Email matth...@strubi.ox.ac.uk > Website http://www.strubi.ox.ac.uk > ----------------------------------------- > > On 3/24/2013 7:46 AM, Appu kumar wrote: > > Thank you for the quick reply. After molecular replacement , i have done > only few cycle of refinement in refmac. I have not done any solvent > modification or NCS averaging. 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. > Please give me your valuable suggestion. I will appreciate your effort. > Thank you > Appu > > On 24 March 2013 02:38, Raji Edayathumangalam <r...@brandeis.edu> wrote: > >> 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 >> >> > >
