Maybe there is a domain shift of your protein compared to the model. If this is the case, try to do the MP with successive domains.
2010/9/13 Paul Holland <[email protected]> > Hello fellow crystallographers, > > I am trying molecular replacement for a protein crystal dataset that has > very high sequence similarity to the search model with several predicted > flexible loop regions; however, all attempts at finding a solution have not > produce very ideal starting solutions using Phaser and Molrep (CC = 0.3 and > Z-score = 5). I am very confident that the unit cell parameters are C2 > 84.027 120.565 108.272 90.00 104.71 90.00, and there appears to be no > evidence of twinning. The Matthews calculation predicts from anywhere from > 2-4 monomers in the ASU, and calculation of the SRF in Molrep does not > identify any peaks in higher order symmetry except for the expected > crystallographic two-fold for C2. Below is the table from the calculated > SRF in molrep. Any advice would be greatly appreciated. > > # theta phi chi alpha beta gamma Rf > Rf/sigma > Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 870.5 > 21.59 > Sol_RF 2 58.61 -10.17 180.00 169.83 -117.23 10.17 162.5 > 4.03 > Sol_RF 3 66.02 -0.00 180.00 180.00 -132.03 0.00 161.1 > 4.00 > Sol_RF 4 58.42 -9.54 180.00 170.46 -116.85 9.54 159.8 > 3.96 > Sol_RF 5 149.84 0.00 180.00 -180.00 60.32 0.00 156.0 > 3.87 > Sol_RF 6 58.96 -5.52 180.00 174.48 -117.91 5.52 151.5 > 3.76 > Sol_RF 7 65.59 20.95 180.00 20.95 131.18 159.05 143.9 > 3.57 > Sol_RF 8 90.00 -98.96 180.00 0.00 180.00 17.92 142.9 > 3.55 > Sol_RF 9 56.53 15.78 180.00 15.78 113.07 164.22 142.0 > 3.52 > Sol_RF 10 71.10 -19.94 180.00 160.06 -142.20 19.94 141.6 > 3.51 > Sol_RF 11 71.28 29.78 180.00 29.78 142.55 150.22 140.4 > 3.48 > Sol_RF 12 65.22 -15.88 180.00 164.12 -130.44 15.88 139.2 > 3.45 > Sol_RF 13 68.84 -0.00 180.00 180.00 -137.67 0.00 138.0 > 3.42 > Sol_RF 14 32.51 -180.00 180.00 -180.00 65.02 -0.00 137.9 > 3.42 > Sol_RF 15 75.02 -28.84 180.00 151.16 -150.04 28.84 134.7 > 3.34 > Sol_RF 16 71.69 -20.99 180.00 159.01 -143.37 20.99 133.0 > 3.30 > Sol_RF 17 92.13 101.46 179.93 102.35 -175.74 79.42 130.9 > 3.25 > Sol_RF 18 107.89 144.73 179.79 145.06 -144.22 35.61 128.8 > 3.19 > Sol_RF 19 87.45 -78.19 180.00 101.81 -174.90 78.19 128.1 > 3.18 > Sol_RF 20 38.57 0.69 30.36 102.66 -18.79 -78.71 122.4 > 3.04 > Sol_RF 21 26.77 174.59 176.58 172.68 53.52 3.49 120.5 > 2.99 > Sol_RF 22 116.66 178.08 175.14 3.49 126.48 187.32 120.5 > 2.99 > Sol_RF 23 75.56 -41.35 180.00 138.65 -151.12 41.35 119.8 > 2.97 > Sol_RF 24 66.12 36.35 180.00 36.35 132.24 143.65 116.6 > 2.89 > Sol_RF 25 83.87 71.62 180.00 71.62 167.74 108.38 114.7 > 2.85 > Sol_RF 26 69.24 -12.37 180.00 167.63 -138.48 12.37 112.3 > 2.79 > Sol_RF 27 59.75 15.26 172.29 7.64 119.07 157.12 112.2 > 2.78 > Sol_RF 28 120.25 -164.74 172.29 22.88 119.07 172.36 112.2 > 2.78 > Sol_RF 29 96.68 -70.99 180.00 109.01 -166.63 70.99 110.9 > 2.75 > Sol_RF 30 63.23 -44.73 180.00 135.27 -126.47 44.73 108.9 > 2.70 > > Cheers, > > Paul Holland > > > -- Yu Zhang HHMI associate Waksman Institute Rutgers University
