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1) Are you sure your model is only a monomer alone? 2) The first 4 rotation peaks indicate there is probably a trimer, and in the same orientation probably as the one in the native. rotation peak 1 and 2 generate almost the identity matrix. What are the cells for the 2 forms? Eleanor 11/08/2010 12:25 PM, intekhab alam wrote: > Hi, There > > 1.I have collected two data sets one for the native protein (60Kda) and > complex of native with other protein of 8 Kda. The shape of native dataset > is cubic while that of the complexed one is triangular. A number of dataset > were collected for these two and i successfully indexed them to a spacegroup > of C2. > > 2.While doing molecular replacement for the native data using a monomeric > template clear solution with 3 monomers in the asyymetric unit was obtained > and structure solved successfully with R/rfee of 19/23 at 2.5A reolution. > > 3.The molecular replacement of the complexed dataset with the same template > gave a solution with 2 monomers in asymmetric unit with a lot of clashes > between the two subnuints. when i closely examined the logfile i observed > that there was pseudotranslation detected by the program in all of my > complex dataset. I run xtiage as well as pointless and truncate which rules > out any twinning as well as wrong space group assignment. Pseudotranslation > of 18% has been detected by balbes. > > 4. I also run the Balbes at Murshodov server which gave a solution with 4 > monomers in the asymmetric but still showing a lot of clashes in the > asymmetric unit (R/Rfree 0.43/0.47) followed by automatic refinemnet with > Arp/wARp which gave a model . When i examine the density of the model i saw > a lot of clashes in the asymmetric unit but the density are interpretable so > that bakbone can be easily modelled. But the R and R free donot goes down > from (R/Rfree 0.43/0.47) > > I have pasted the logfile below from molrep for your convenience. Kindly > suggest me how can i proceed with this dataset. That will be very kind of > you if you spend some time over my problem. Another question , is it > possible that this pseudotranslation is due to the smaller protein of the > complex which has slightly changed the crystal packing. ( SDS done on the > complex crystals clearly showed the presence of both the proteins). > > > > > --- Check Patterson for pseudo-translation --- > PST_limit : 0.125 of origin peak > INFO: pseudo-translation was detected. > Origin Patterson peak: P,P/sig : 80563.180 266.237 > 1 Patterson. peak : p,P/sig : 80560.719 266.228 > 2 Patterson peak : P,P/sig : 13992.708 46.242 > 3 Patterson peak : P,P/sig : 13992.708 46.242 > Peak 1: trans.vector /ort/ : 60.164 98.423 > 0.000 > trans.vector /frac/: 0.500 0.500 > 0.000 > Peak 2: trans.vector /ort/ : 31.861 0.000 > 0.000 > trans.vector /frac/: 0.265 0.000 > 0.000 > Peak 3: trans.vector /ort/ : 28.303 98.423 > 0.000 > trans.vector /frac/: 0.235 0.500 > 0.000 > INFO: translation vector of peak 2 will be used. > WARNING: with keyword: PST --> MODE = F , STICK = N > > Sol_ Space group : C 1 2 1 > Sol_ No: 5 Sett: 2 > Sol_ Cell: 120.328 196.846 109.285 90.00 113.84 90.00 > > Sol_--- Rotation function --- > Sol_ > Radius of gyration : 23.58 > Sol_ Radius of integration : 47.16 > Sol_ Resmin,Resmax : 48.03 2.42 > WARNING: For this radius integration program uses data included > between 48.0 and 2.71 (angstrom..) > --- rfcoef for model --- > --- rfcoef for Fobs --- > NCS (from Self rotation Function): 1 > NCS_model (from Model Self rotation Function): 1 > Program will use NCS_model =: 1 > > Number of RF peaks : 30 > theta phi chi alpha beta gamma Rf > Rf/sigma > Sol_RF 1 106.45 50.40 1.37 320.21 1.31 39.41 0.9325E+05 > 19.98 > Sol_RF 2 0.00 0.00 0.00 0.00 0.00 0.00 0.8668E+05 > 18.57 > Sol_RF 3 158.10 -1.79 120.96 209.61 37.87 33.18 0.8147E+05 > 17.46 > Sol_RF 4 22.21 -179.07 120.40 149.19 38.30 327.33 0.7596E+05 > 16.28 > Sol_RF 5 0.83 144.00 179.87 143.94 1.66 35.93 0.4234E+05 > 9.07 > Sol_RF 6 146.73 90.95 73.37 329.03 38.27 327.14 0.3574E+05 > 7.66 > Sol_RF 7 0.00 0.00 179.92 97.16 0.00 82.76 0.3504E+05 > 7.51 > Sol_RF 8 34.01 88.19 71.45 29.00 38.12 32.61 0.3354E+05 > 7.19 > Sol_RF 9 77.12 174.71 90.84 97.45 87.95 288.04 0.2136E+05 > 4.58 > Sol_RF 10 134.42 132.29 7.11 39.81 5.07 315.22 0.2089E+05 > 4.48 > Sol_RF 11 152.93 177.57 136.00 21.98 49.92 206.84 0.1861E+05 > 3.99 > Sol_RF 12 156.31 -169.21 19.45 91.88 7.78 250.29 0.1849E+05 > 3.96 > Sol_RF 13 130.28 116.07 92.63 351.98 66.96 299.83 0.1810E+05 > 3.88 > Sol_RF 14 0.00 0.00 11.30 11.30 0.00 0.00 0.1808E+05 > 3.87 > Sol_RF 15 36.79 -89.11 90.53 219.84 50.36 218.06 0.1801E+05 > 3.86 > Sol_RF 16 134.90 -102.85 173.11 82.03 90.00 107.72 0.1761E+05 > 3.77 > Sol_RF 17 106.06 0.94 54.00 262.92 51.73 81.03 0.1753E+05 > 3.76 > Sol_RF 18 135.11 85.04 162.00 277.64 88.39 287.56 0.1728E+05 > 3.70 > Sol_RF 19 127.04 109.26 97.92 344.58 74.03 306.06 0.1722E+05 > 3.69 > Sol_RF 20 141.26 -144.07 13.23 120.76 8.27 228.90 0.1705E+05 > 3.65 > Sol_RF 21 142.16 -164.54 114.88 54.42 62.26 203.50 0.1675E+05 > 3.59 > Sol_RF 22 137.57 -150.27 12.10 115.26 8.16 235.79 0.1657E+05 > 3.55 > Sol_RF 23 162.01 178.37 129.40 24.79 32.42 208.06 0.1654E+05 > 3.54 > Sol_RF 24 135.22 28.82 14.02 293.83 9.86 56.20 0.1636E+05 > 3.51 > Sol_RF 25 134.21 84.96 161.20 278.32 90.00 288.40 0.1621E+05 > 3.47 > Sol_RF 26 43.85 57.57 90.92 3.81 59.17 68.66 0.1616E+05 > 3.46 > Sol_RF 27 22.55 173.85 110.70 137.04 36.79 329.34 0.1615E+05 > 3.46 > Sol_RF 28 142.62 94.57 75.18 333.11 43.47 323.97 0.1612E+05 > 3.46 > Sol_RF 29 25.92 179.07 113.06 142.75 42.77 324.61 0.1609E+05 > 3.45 > Sol_RF 30 128.76 -103.39 65.70 144.60 50.05 171.38 0.1599E+05 > 3.43 > Final number of peaks : 30 > INFO: Relations between peaks see in molrep.doc > Time: 22h 12m 3s Elapsed: 0h 3m 46s > Sol_ > Sol_--- Translation function --- > Sol_ Resmin,Resmax : 48.03 2.42 > Sol_ NCS model : 1 > --- List of psewdo-translation vectors --- > PST_vector 1: 0.265 0.000 0.000 > --- > > Time_elapsed: 0h 4m 1s Remained: 0h 7m 15s > Sol_ RF TF Tf/sig TFcntrst PFind PF PFmin wRfac Scor Scor_max > Cntrst > Sol___1__1 24.83 10.203 1.00 1.00 -4.18 0.595 0.390 0.390 > 0.00 > Sol___2__1 21.58 11.436 1.00 1.00 -4.13 0.601 0.377 0.390 > 0.00 > Sol___3_14 4.093 4.995 1.00 1.00 -3.57 0.614 0.353 0.390 > 0.00 > Sol___4__1 21.04 13.251 1.00 0.98 -3.46 0.607 0.361 0.390 > 0.00 > Sol___5__1 14.68 3.760 1.00 1.00 -3.25 0.614 0.349 0.390 > 3.99 > Sol___6__6 5.017 0.269 1.00 1.00 -4.19 0.625 0.325 0.390 > 3.14 > Sol___7__1 13.18 3.772 1.00 1.00 -3.18 0.617 0.342 0.390 > 3.14 > Sol___8__6 4.372 2.119 1.00 1.00 -3.86 0.622 0.332 0.390 > 3.02 > Sol___9__3 4.122 2.055 1.00 1.00 -3.41 0.626 0.318 0.390 > 3.20 > Sol__10__2 4.511 1.500 1.00 1.00 -3.91 0.627 0.317 0.390 > 2.96 > Sol__11__2 4.970 2.936 1.00 1.00 -3.99 0.628 0.316 0.390 > 2.79 > Sol__12__5 3.856 1.531 1.00 1.00 -3.73 0.628 0.313 0.390 > 3.01 > Sol__13__6 3.437 1.204 1.00 1.00 -4.07 0.629 0.315 0.390 > 2.92 > INFO: contrast is good enough. Stop this run > > --- Summary --- > > S_ RF TF theta phi chi tx ty tz TFcnt wRfac > Scor > > S___1__1 1 106.45 50.40 1.37 0.352 0.000 0.273 10.20 0.595 > 0.390 > S___2__1 2 0.00 0.00 0.00 0.352 0.000 0.273 11.44 0.601 > 0.377 > S___4__1 3 22.21 -179.07 120.40 0.104 0.000 0.167 13.25 0.607 > 0.361 > S___3_14 4 158.10 -1.79 120.96 0.489 0.000 0.386 5.00 0.614 > 0.353 > S___5__1 5 0.83 144.00 179.87 0.216 0.000 0.272 3.76 0.614 > 0.349 > S___7__1 6 0.00 0.00 179.92 0.216 0.000 0.272 3.77 0.617 > 0.342 > S___8__6 7 34.01 88.19 71.45 0.178 0.000 0.186 2.12 0.622 > 0.332 > S___6__6 8 146.73 90.95 73.37 0.368 0.000 0.225 0.27 0.625 > 0.325 > S___9__3 9 77.12 174.71 90.84 0.482 0.000 0.245 2.06 0.626 > 0.318 > S__10__2 10 134.42 132.29 7.11 0.075 0.000 0.233 1.50 0.627 > 0.317 > S__11__2 11 152.93 177.57 136.00 0.091 0.000 0.216 2.94 0.628 > 0.316 > S__13__6 12 130.28 116.07 92.63 0.473 0.000 0.197 1.20 0.629 > 0.315 > S__12__5 13 156.31 -169.21 19.45 0.084 0.000 0.319 1.53 0.628 > 0.313 > > Contrast = 2.92 > > Sol_ > S_ Nmon RF TF theta phi chi tx ty tz TFcnt wRfac > Scor > S__ 2 1 1 106.45 50.40 1.37 0.352 0.000 0.273 10.20 0.595 > 0.390 > > > PST_vector was used 1: 0.265 0.000 0.000 > --- convert "molrep.crd" to "molrep.pdb" --- >