Sorry for the misconception. Yes i am expanding the space group from merged mtz file. Actually i have enough number of images collected. when i indexed, integrate, and scale the data in either C2221 or P 21, it fetches the overall 98% completeness. But when i am trying to reindex the data from C2221 to P21 keeping the Rfree flag of C2221, the completeness of data reduced drastically to 40%. This is what i am not getting. I am a beginner so i have to read a lot which i am doing also, but i had few practical confusion which i shared and off course i am getting good response. Thank you all for your kind response and educating me on the problem i faced. Thank you all for your valuable response.
On 24 March 2013 15:15, vellieux <frederic.velli...@ibs.fr> wrote: > Hello, > > Here we deal with symmetry and the unique part of reciprocal space (the > reciprocal space "asymmetric unit" so to speak). > > C222(1) has eight asymmetric units (international tables, space group 20); > > P2(1) only has two. Assuming that Friedel's law does apply, then the > minimum rotation range to collect a non-redundant data set (one observation > per reflection) is 90 degrees, provided that the crystal is "correctly" and > perfectly aligned. Normally with our current data collection methods where > the crystal is randomly oriented, we would collect more than 90 degrees > (180 degrees, or 360 degrees with the Pilatus detectors on an intense SR > beamline where you cannot really check during data collection how well the > crystal fares during exposure to the X-rays - "shoot first, think later". > > The "reciprocal space" asymmetric unit in C222(1) is smaller. > > I assume that what you are doing is to take the reduced data set file (an > MTZ file probably) and reduce the symmetry from C222(1) to P2(1). You will > not cover the monoclinic reciprocal space asymmetric unit by doing so. > > The way to do it is to take the file from processing, before > (crystallographic symmetry) merging of the equivalents, and perform the > scaling and merging in the P2(1) space group. Or reprocess the data frames > in P2(1) if you have lost the unmerged data file. > > Now of course this will still give you a poor completeness if you have > used a strategy to optimize data collection in the orthorhombic space group > (you won't have collected enough data then for good completeness in the > monoclinic space group). > > I hope this is clear ! > > HTH, > > Fred. > > > On 24/03/13 11:20, Appu kumar wrote: > > 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 >>> >>> >> >> > > > -- > Fred. Vellieux (B.Sc., Ph.D., hdr) > ouvrier de la recherche > IBS / ELMA > 41 rue Jules Horowitz > F-38027 Grenoble Cedex 01 > Tel: +33 438789605 > Fax: +33 438785494 > >
