Dears, I am sorry for not saying it clearly. By looking at the 00l lines and by Phenix.xtrige, it is probable P6122 or P6522. In the molecular replacement searching, I have set to search all the possible of space group of P622 in Phaser and Molrep. But all the trials failed. My model is the structure large subunit of the complex. So the sequence identity is 100%. The large subunit is composed by two domains. So in the search, I divided the model into two parts. Any other suggestions?
Thanks and best wishes. On Tue, Jul 14, 2009 at 8:11 PM, Randy Read <rj...@cam.ac.uk> wrote: > Hi, > > You didn't say whether you are absolutely certain that it is P622 (i.e. you > have measured complete data for all the h00, 0k0 and 00l lines and found no > systematic absences) or whether it could be another space group with the > same Laue symmetry. Unless you're absolutely certain, then you have to try > all possible choices of space group. In fact, I'd be surprised to see such > a long c cell edge if there is no screw axis, but unsurprised if it were > (say) a 6(1) screw axis. > > The other thing you didn't mention is how good you expect your models to > be. How high is the sequence identity between the model and the target for > each component? Could there be flexibility in the molecules? > > Good luck! > > Randy Read > > On 14 Jul 2009, at 12:23, Wei Zhang wrote: > > Dears, >> I am doing molecular replacement of a protein complex with a P622 data set >> with large cell parameters (a=b=135, c=480). The data set seems well. R >> merge is 0.17 for all and 0.70 for the last shell of 2.9 angstrom. I am not >> sure it is a complex in the crystal. Phenix analysis reveal there is no >> twin. The proposed protein complex is about 70 kDa with a larger subunit of >> 50 kDa and a small subunit of 20 kDa. The matthews analysis indicates that >> there might be 3 complexes in the ASU. The structure of the 50 kDa subunit >> is known while the 20 kDa one is unknown. But molecular replacement failed >> with either Phaser or Molrep. >> Self-rotation with CNS reported the result as below: >> ! index, psi, phi, kappa, RF-function ( 0.25) >> 1 0.000 0.000 180.000 29.7217 >> Self-ratation with Molrep reported the result as below: >> Number of RF peaks : 30 >> theta phi chi alpha beta gamma Rf >> Rf/sigma >> Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 0.3444E+05 >> 17.13 >> Sol_RF 2 90.00 -80.07 179.99 0.00 180.00 -19.86 5061. >> 2.52 >> Sol_RF 3 90.00 -65.53 179.99 0.00 180.00 -48.94 4890. >> 2.43 >> Sol_RF 4 90.00 -76.12 179.99 0.00 180.00 -27.76 4722. >> 2.35 >> Sol_RF 5 11.42 90.00 61.00 30.00 11.53 30.00 2438. >> 1.21 >> Sol_RF 6 164.38 60.00 179.99 60.00 -31.24 120.00 1850. >> 0.92 >> Sol_RF 7 85.13 -141.54 179.97 38.32 -170.26 141.40 1805. >> 0.90 >> Sol_RF 8 90.00 -60.00 90.00 30.00 -90.00 -30.00 1764. >> 0.88 >> Sol_RF 9 84.07 -144.87 179.96 34.98 -168.15 144.73 1743. >> 0.87 >> Sol_RF 10 72.25 -60.00 89.30 46.76 -84.03 -13.24 1665. >> 0.83 >> Sol_RF 11 138.24 -130.77 180.00 49.23 83.52 130.77 1608. >> 0.80 >> Sol_RF 12 170.36 30.00 179.99 30.00 -19.28 150.00 1590. >> 0.79 >> Sol_RF 13 82.04 60.00 179.99 60.00 -164.07 120.00 1571. >> 0.78 >> Sol_RF 14 141.01 30.00 179.99 30.00 -77.99 150.00 1554. >> 0.77 >> Sol_RF 15 123.63 -155.38 179.98 24.62 112.74 155.38 1517. >> 0.75 >> Sol_RF 16 148.80 30.00 179.99 30.00 -62.39 150.00 1450. >> 0.72 >> Sol_RF 17 142.61 30.00 180.00 30.00 -74.78 150.00 1439. >> 0.72 >> Sol_RF 18 72.25 -150.00 179.99 30.00 -144.50 150.00 1422. >> 0.71 >> Sol_RF 19 47.42 -120.00 179.98 60.00 -94.83 120.00 1417. >> 0.71 >> Sol_RF 20 153.12 30.00 179.98 30.00 -53.75 150.00 1292. >> 0.64 >> Sol_RF 21 155.99 30.00 179.98 30.00 -48.01 150.00 1274. >> 0.63 >> Sol_RF 22 138.05 30.00 179.99 30.00 -83.91 150.00 1258. >> 0.63 >> Sol_RF 23 54.12 120.00 89.15 60.00 69.32 0.00 1254. >> 0.62 >> Sol_RF 24 129.04 -136.48 179.99 43.52 101.93 136.48 1193. >> 0.59 >> Sol_RF 25 138.65 -164.29 179.99 15.71 82.69 164.29 1185. >> 0.59 >> Sol_RF 26 84.16 51.37 179.98 51.37 -168.32 128.63 1176. >> 0.59 >> Sol_RF 27 90.00 150.00 59.82 60.00 59.82 -60.00 1162. >> 0.58 >> Sol_RF 28 43.66 -133.74 179.98 46.26 -87.31 133.74 1161. >> 0.58 >> Sol_RF 29 127.85 -169.33 179.99 10.67 104.29 169.33 1153. >> 0.57 >> Sol_RF 30 124.15 30.00 179.99 30.00 -111.71 150.00 1147. >> 0.57 >> >> My question is: >> 1. For a 70 kDa protein compelx, is it common to have such a large cell >> with a dimention as long as 480 angstrom? >> 2. Is it possible that the longest dimention of cell is doubled? If it is, >> how to divide it? >> 3. How to interpret the self-rotation results. The results from CNS and >> Molrep differs so much. >> 4. Any other suggestions on the molecular replacement are appraciated. >> >> Thanks. >> >> Wei Zhang >> PKU >> >> >> > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > >
