Dear All: I try to use Phaser to solve the structure by Molecular Replacement.
The data set is collected @180 degree. I process the data using HKL, and have resonable good score: rejection (0.05), Linear R-factor (0.038), completeness (98.3), resolution (50-1.5). I then use Phaser to do MR. The parameter setting are: automated search components in asymmetric unit; number of residue 1332; number in asymmetric unit 1 perform search search using "ensemble1" number of copies to search for 4 The protein is in tetramer form. I define this by using the residue number (1332) which is 4 x monomer. After run, Phaser only gave 9 partial solutions, and no solution with all components. The resulted PDB contains only dimer form of the protein, not the tetramer. And the first TFZ score is around 2.5, which is too low for MR. I have the report file of data processing and the summary of Phaser attached. Could you please advice which part is wrong, why can I get the tetramer form of the protein? Thank you Uma
Crystal - Global Refinement
*Space Group* P2
*Resolution Processing* 50.00 - 1.52
*Resolution Scaling* 50.00 - 1.52
*a* 79.70 ± 0.01
*b* 125.27 ± 0.01
*c* 83.60 ± 0.01
*alpha* 90.000 ±
*beta* 118.02 ± 0.05
*gamma* 90.000 ±
*Volume* 736873.6
*Mosaicity Range* 0.20 - 0.34
Global Statistics
*Crystal* crystal1
*Date* Aug 01, 2012
*Experimenter* KP
*Rawdata directory* /home/KP/Desktop/BY/0712/process-0712/data/CD6_7
*Processing directory* /home/KP
*Data files* CD6_7_1_0001.cbf[1-180]
*Wavelength* 0.97920
*Total Number of Reflections* 728105
*Number of Unique Reflections* 220394
*Number of Reflections Marked for Rejection* 346
*Percentage of Reflections Marked for Rejection* 0.05
*Percentage of Reflections Rejected* 0.00
*Linear R-factor in shell <50.00 - 4.13>* 0.038
*Change of B-factor* -0.40 - 8.33
*Completeness* 98.3
*Completeness in shell <1.55 - 1.52>* 91.9
*Mean I/sigma* 10.5
*Mean I/sigma in shell <1.55 - 1.52>* 0.7
*Total Linear R-Merge* 0.094
Site Information
*Detector* CCD pilatusCBF
*Polarization* 0.99
*X Beam Position* 217.5
*Y Beam Position* 219.5
*Cassette Rotation X* 0.00
*Cassette Rotation Y* 0.00
*Cassette Rotation Z* 0.00
*Yscale* 1.0
*Skew* 0.0
*Crossfire X* 0.00
*Crossfire Y* 0.00
*Crossfire XY* 0.00
Scale and B vs. Frame
Chi^2 and R-Factor vs. Frame
*Frame Number* *Scale* *B* *Chi^2* *R-factor*
1 10.91589 -0.40 1.185 0.082
2 10.77627 -0.38 1.234 0.082
3 10.53368 -0.33 1.162 0.083
4 10.36566 -0.27 1.162 0.079
5 10.32651 -0.19 1.064 0.077
6 10.18485 -0.10 1.030 0.075
7 10.00000 0.00 1.076 0.076
8 10.05111 0.10 1.013 0.078
9 9.92706 0.21 0.995 0.076
10 9.83898 0.31 0.952 0.075
11 9.64515 0.42 0.907 0.077
12 9.61982 0.53 0.880 0.076
13 9.61376 0.63 0.885 0.069
14 9.44380 0.74 0.834 0.073
15 9.44114 0.85 0.765 0.068
16 9.29782 0.96 0.834 0.069
17 9.21481 1.08 0.750 0.067
18 9.12255 1.18 0.737 0.071
19 9.15504 1.28 0.798 0.073
20 9.06806 1.38 0.795 0.076
21 9.03864 1.47 0.740 0.074
22 8.96390 1.57 0.793 0.070
23 8.87753 1.66 0.759 0.073
24 8.81280 1.76 0.774 0.076
25 8.80572 1.84 0.777 0.073
26 8.64398 1.93 0.825 0.079
27 8.56313 2.02 0.796 0.074
28 8.58220 2.11 0.720 0.073
29 8.45429 2.19 0.763 0.074
30 8.43629 2.27 0.746 0.072
31 8.37449 2.34 0.821 0.081
32 8.32575 2.41 0.767 0.069
33 8.23116 2.47 0.848 0.080
34 8.25275 2.53 0.717 0.080
35 8.20440 2.57 0.734 0.073
36 8.12370 2.62 0.788 0.079
37 8.10550 2.66 0.777 0.077
38 8.04424 2.70 0.726 0.077
39 7.98665 2.74 0.760 0.077
40 7.92014 2.77 0.692 0.079
41 7.94125 2.81 0.711 0.079
42 7.89751 2.85 0.760 0.078
43 7.91178 2.90 0.650 0.079
44 7.84116 2.94 0.692 0.078
45 7.80008 2.99 0.737 0.077
46 7.78514 3.03 0.658 0.076
47 7.79019 3.07 0.656 0.077
48 7.77994 3.10 0.651 0.081
49 7.76673 3.14 0.567 0.077
50 7.71487 3.18 0.630 0.079
51 7.64531 3.22 0.631 0.082
52 7.65363 3.26 0.586 0.082
53 7.69821 3.31 0.604 0.080
54 7.67023 3.36 0.589 0.083
55 7.66701 3.42 0.550 0.082
56 7.67157 3.47 0.544 0.080
57 7.66821 3.52 0.609 0.087
58 7.67582 3.57 0.550 0.084
59 7.70985 3.63 0.572 0.086
60 7.69346 3.68 0.553 0.084
61 7.75456 3.73 0.550 0.083
62 7.73917 3.79 0.546 0.082
63 7.76342 3.84 0.553 0.081
64 7.78951 3.89 0.534 0.087
65 7.82720 3.94 0.528 0.089
66 7.88353 4.00 0.517 0.087
67 7.90148 4.06 0.504 0.082
68 7.90870 4.12 0.512 0.091
69 7.93080 4.18 0.522 0.087
70 7.98669 4.23 0.518 0.089
71 8.01498 4.29 0.504 0.090
72 7.98602 4.35 0.520 0.092
73 8.15680 4.40 0.524 0.094
74 8.21260 4.45 0.543 0.091
75 8.27562 4.50 0.537 0.094
76 8.35224 4.56 0.494 0.089
77 8.37099 4.61 0.496 0.094
78 8.46624 4.67 0.518 0.093
79 8.58367 4.72 0.504 0.094
80 8.67996 4.77 0.520 0.092
81 8.68223 4.82 0.483 0.099
82 8.78507 4.87 0.529 0.096
83 8.90363 4.92 0.513 0.101
84 8.99475 4.97 0.528 0.098
85 9.11664 5.01 0.553 0.096
86 9.26082 5.04 0.521 0.094
87 9.30406 5.08 0.534 0.096
88 9.43619 5.10 0.537 0.103
89 9.56206 5.12 0.524 0.096
90 9.76314 5.14 0.516 0.096
91 9.90511 5.15 0.509 0.096
92 10.06852 5.16 0.514 0.099
93 10.18187 5.16 0.538 0.102
94 10.29450 5.15 0.537 0.095
95 10.43472 5.14 0.524 0.093
96 10.66126 5.13 0.535 0.098
97 10.88999 5.11 0.538 0.097
98 11.03551 5.10 0.535 0.096
99 11.26758 5.08 0.521 0.090
100 11.27732 5.06 0.541 0.095
101 11.57325 5.03 0.537 0.096
102 11.70433 5.02 0.549 0.095
103 11.91664 4.99 0.540 0.092
104 12.09329 4.96 0.566 0.089
105 12.30229 4.92 0.548 0.090
106 12.48413 4.89 0.545 0.093
107 12.72518 4.85 0.531 0.089
108 12.82509 4.82 0.572 0.090
109 12.99964 4.79 0.565 0.089
110 13.17812 4.76 0.552 0.092
111 13.35523 4.72 0.584 0.090
112 13.50925 4.69 0.546 0.087
113 13.62776 4.65 0.583 0.088
114 13.86639 4.62 0.578 0.089
115 14.07207 4.58 0.567 0.087
116 14.21558 4.55 0.577 0.088
117 14.39626 4.52 0.580 0.089
118 14.49770 4.49 0.568 0.085
119 14.71481 4.46 0.592 0.085
120 14.79127 4.43 0.586 0.086
121 14.89855 4.40 0.590 0.082
122 15.04468 4.38 0.585 0.086
123 15.18924 4.36 0.573 0.081
124 15.29296 4.35 0.674 0.090
125 15.36051 4.34 0.609 0.081
126 15.40375 4.32 0.605 0.085
127 15.35487 4.32 0.603 0.085
128 15.34417 4.32 0.596 0.084
129 15.42148 4.33 0.589 0.081
130 15.37074 4.34 0.603 0.085
131 15.38334 4.35 0.583 0.086
132 15.32908 4.36 0.592 0.087
133 15.15193 4.38 0.598 0.086
134 15.32769 4.40 0.601 0.084
135 15.21145 4.43 0.601 0.084
136 15.20317 4.47 0.605 0.083
137 15.06638 4.53 0.595 0.089
138 14.94010 4.58 0.584 0.090
139 14.98296 4.63 0.600 0.087
140 14.85197 4.69 0.632 0.089
141 14.76225 4.76 0.607 0.091
142 14.63103 4.83 0.607 0.091
143 14.44369 4.91 0.664 0.091
144 14.42410 5.00 0.629 0.095
145 14.27209 5.09 0.610 0.094
146 14.11898 5.18 0.617 0.096
147 13.87514 5.28 0.633 0.099
148 13.74233 5.37 0.655 0.100
149 13.52470 5.47 0.641 0.103
150 13.44363 5.57 0.642 0.106
151 13.38575 5.67 0.605 0.106
152 13.23671 5.78 0.660 0.110
153 12.97711 5.89 0.637 0.105
154 12.81154 6.00 0.675 0.109
155 12.65051 6.12 0.678 0.114
156 12.43508 6.23 0.685 0.112
157 12.23658 6.35 0.714 0.115
158 12.06467 6.46 0.720 0.123
159 11.95329 6.58 0.743 0.121
160 11.65858 6.69 0.751 0.122
161 11.50427 6.80 0.804 0.128
162 11.39428 6.91 0.778 0.132
163 11.26335 7.02 0.804 0.127
164 11.06100 7.13 0.800 0.137
165 10.85951 7.25 0.833 0.142
166 10.81420 7.35 0.865 0.143
167 10.68320 7.46 0.840 0.142
168 10.47695 7.56 0.813 0.147
169 10.35760 7.67 0.850 0.153
170 10.18149 7.76 0.860 0.162
171 10.06132 7.85 0.894 0.147
172 9.89382 7.95 0.852 0.156
173 9.71079 8.03 0.884 0.160
174 9.64244 8.10 0.907 0.157
175 9.49705 8.17 0.935 0.158
176 9.40940 8.22 0.943 0.165
177 9.24530 8.26 0.912 0.166
178 9.13421 8.29 1.010 0.179
179 8.92917 8.32 0.965 0.168
180 8.81981 8.33 0.874 0.168
Completeness vs. Resolution
*Resolution* *I/sigma > 20* *I/sigma > 10* *I/sigma > 5* *I/sigma > 3*
*All Reflections*
27.07 65.5 92.1 96.8 97.9 99.0
3.70 57.2 87.1 94.3 96.0 97.8
3.06 38.4 78.3 90.5 94.5 99.2
2.73 18.1 62.0 82.6 89.0 97.8
2.50 8.4 51.3 76.6 85.7 98.6
2.34 5.9 44.8 73.1 83.8 99.3
2.21 4.0 38.1 67.1 79.6 99.2
2.11 1.7 26.8 56.3 71.6 98.0
2.02 0.8 19.1 49.5 66.8 98.5
1.95 0.4 13.4 41.3 59.6 99.0
1.89 0.1 8.3 33.3 52.3 99.1
1.83 0.0 5.1 24.9 44.2 99.1
1.77 0.0 2.2 16.4 33.4 98.6
1.73 0.0 0.9 11.7 26.5 98.1
1.69 0.0 0.6 8.8 22.2 98.8
1.65 0.0 0.2 6.0 17.9 98.9
1.62 0.0 0.1 3.9 13.4 99.1
1.58 0.0 0.0 2.5 10.2 98.6
1.56 0.0 0.0 1.9 8.5 97.7
1.54 0.0 0.0 1.1 5.4 91.9
Chi^2 and R-Factor vs. Resolution
*Resolution* *Chi^2 T* *R-factor T* *Chi^2 F* *R-factor F*
27.07 0.957 0.029 0.758 0.031
3.70 1.272 0.039 1.026 0.041
3.06 1.135 0.052 0.949 0.056
2.73 1.002 0.066 0.855 0.070
2.50 0.832 0.078 0.740 0.085
2.34 0.825 0.089 0.757 0.099
2.21 0.832 0.102 0.772 0.114
2.11 0.856 0.120 0.805 0.133
2.02 0.785 0.148 0.743 0.164
1.95 0.739 0.175 0.699 0.197
1.89 0.669 0.207 0.647 0.237
1.83 0.611 0.256 0.600 0.293
1.77 0.550 0.317 0.546 0.366
1.73 0.532 0.390 0.524 0.439
1.69 0.507 0.459 0.508 0.524
1.65 0.483 0.526 0.487 0.612
1.62 0.468 0.613 0.470 0.714
1.58 0.449 0.692 0.459 0.813
1.56 0.452 0.715 0.451 0.830
1.54 0.461 0.738 0.456 0.848
I/Sigma and I vs. Resolution
*Resolution* *I* *I/Sigma*
27.07 244.7 27.81
3.70 227.2 25.53
3.06 118.8 20.84
2.73 70.4 15.30
2.50 53.5 12.74
2.34 46.6 11.37
2.21 41.3 10.07
2.11 34.4 7.82
2.02 27.1 6.61
1.95 21.5 5.51
1.89 16.5 4.46
1.83 12.8 3.56
1.77 9.5 2.57
1.73 8.0 2.11
1.69 6.8 1.84
1.65 5.8 1.53
1.62 5.0 1.28
1.58 4.2 1.05
1.56 3.9 0.91
1.54 3.7 0.73
Chi^2 and R-factor vs. Average I
*Average I* *Chi^2* *R-factor*
-10.0 0.451 0.000
38.1 0.501 0.438
145.3 0.662 0.170
289.6 0.849 0.118
574.9 1.041 0.088
1144.2 1.174 0.068
2273.7 1.185 0.054
4536.3 1.094 0.043
9002.4 0.903 0.034
17616.4 0.830 0.028
34772.7 0.806 0.026
68363.5 0.858 0.025
134242.7 1.006 0.023
283887.3 1.569 0.030
Average and Cumulative Redundancy vs. Resolution
*Resolution* *Average Redundancy* *Redundancy >= 2* *Redundancy >=
3* *Redundancy >= 4* *Redundancy >= 7-8*
27.07 1.8 98.2 81.3 72.7 0.0
3.70 1.8 96.1 72.6 64.3 0.0
3.06 1.9 98.7 84.8 77.0 0.0
2.73 1.8 96.2 72.6 62.9 0.0
2.50 1.8 97.6 77.7 68.4 0.0
2.34 1.8 98.2 81.7 71.5 0.0
2.21 1.9 98.4 83.7 73.8 0.0
2.11 1.7 94.9 69.5 54.1 0.0
2.02 1.8 96.6 75.3 62.4 0.0
1.95 1.8 97.3 79.4 67.0 0.0
1.89 1.8 97.7 81.3 68.8 0.0
1.83 1.9 97.9 82.3 70.8 0.0
1.77 1.8 96.3 75.7 60.5 0.0
1.73 1.7 94.7 70.8 52.2 0.0
1.69 1.8 97.0 77.0 61.4 0.0
1.65 1.8 97.0 79.0 63.7 0.0
1.62 1.8 97.2 78.2 61.2 0.0
1.58 1.7 95.5 74.5 53.7 0.0
1.56 1.7 90.1 65.8 40.8 0.0
1.54 1.5 72.2 42.4 19.1 0.0
Set 1. /home/KP/Desktop/BY/0712/process-0712/data/CD6_7/CD6_7_1_0###.cbf
234_phaser_MR_sum.log
Description: Binary data
