Software | Name | Version | Classification | NB |
---|
DENZO | | data reduction | SCALEPACK | | data scaling | PHENIX | 1.7.3_928refinement | PDB_EXTRACT | 3.1 | data extraction | CBASS | | data collection | PHENIX | 1.7.3_928phasing | | | | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.203 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.7765 / σ(F): 1.36 / Phase error: 29.85 / Stereochemistry target values: TWIN_LSQ_F
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.1777 | 2616 | 5.14 % | RANDOM |
---|
Rwork | 0.1467 | - | - | - |
---|
obs | 0.1483 | 50869 | 91.35 % | - |
---|
|
---|
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.01 Å2 / ksol: 0.377 e/Å3 |
---|
Displacement parameters | Biso max: 119.17 Å2 / Biso mean: 26.2909 Å2 / Biso min: 6.17 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -2.2223 Å2 | 0 Å2 | 0.1262 Å2 |
---|
2- | - | 0.8726 Å2 | -0 Å2 |
---|
3- | - | - | 1.3496 Å2 |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 1.95→46.203 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 5442 | 0 | 49 | 241 | 5732 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.006 | 5625 | X-RAY DIFFRACTION | f_angle_d1.094 | 7597 | X-RAY DIFFRACTION | f_chiral_restr0.072 | 827 | X-RAY DIFFRACTION | f_plane_restr0.004 | 975 | X-RAY DIFFRACTION | f_dihedral_angle_d13.936 | 2077 | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
---|
1.9505-1.988 | 0.2431 | 73 | 0.1844 | 1570 | 1643 | 51 | 1.988-2.0286 | 0.2289 | 94 | 0.176 | 1836 | 1930 | 60 | 2.0286-2.0727 | 0.2176 | 105 | 0.178 | 2080 | 2185 | 67 | 2.0727-2.1209 | 0.1677 | 137 | 0.1804 | 2265 | 2402 | 74 | 2.1209-2.1739 | 0.213 | 117 | 0.1617 | 2554 | 2671 | 82 | 2.1739-2.2327 | 0.2207 | 146 | 0.1681 | 2740 | 2886 | 89 | 2.2327-2.2984 | 0.2189 | 134 | 0.1729 | 2895 | 3029 | 94 | 2.2984-2.3726 | 0.197 | 164 | 0.1603 | 2969 | 3133 | 95 | 2.3726-2.4574 | 0.195 | 155 | 0.1654 | 2989 | 3144 | 95 | 2.4574-2.5558 | 0.2125 | 134 | 0.164 | 2903 | 3037 | 96 | 2.5558-2.6721 | 0.1782 | 148 | 0.1614 | 2922 | 3070 | 95 | 2.6721-2.8129 | 0.1992 | 159 | 0.1694 | 2940 | 3099 | 95 | 2.8129-2.9891 | 0.1725 | 173 | 0.1509 | 2928 | 3101 | 94 | 2.9891-3.2199 | 0.1986 | 166 | 0.1515 | 2928 | 3094 | 95 | 3.2199-3.5438 | 0.1622 | 170 | 0.1278 | 2928 | 3098 | 95 | 3.5438-4.0562 | 0.147 | 167 | 0.1156 | 2943 | 3110 | 95 | 4.0562-5.1092 | 0.1405 | 166 | 0.1042 | 2929 | 3095 | 95 | 5.1092-43.9398 | 0.1801 | 179 | 0.1633 | 2961 | 3140 | 94 |
|
---|
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
---|
1 | 0.4494 | 0.2347 | -0.1385 | 0.4198 | -0.2625 | 1.6257 | -0.0849 | 0.0175 | -0.0242 | 0.2197 | 0.121 | 0.1835 | -0.009 | -0.1289 | -0.2367 | 0.2721 | 0.0296 | 0.1831 | 0.077 | 0.1093 | 0.0714 | -25.0904 | -22.3628 | 66.0495 | 2 | 1.3182 | 0.6635 | -0.6592 | 1.61 | -1.1349 | 1.4646 | -0.1519 | 0.0592 | -0.1287 | 0.1008 | 0.0901 | 0.1319 | 0.2148 | -0.1231 | -0.0001 | 0.2039 | 0.0042 | 0.137 | 0.0524 | 0.0075 | 0.1047 | -20.6357 | -32.0605 | 63.888 | 3 | 1.8357 | -0.3192 | 2.6503 | 2.4452 | 0.2563 | 6.7227 | -0.0957 | -0.0211 | 0.1035 | 0.189 | 0.0642 | -0.207 | -0.4228 | 0.4943 | 0.0331 | 0.1594 | -0.0685 | -0.0414 | 0.1467 | 0.0092 | 0.0253 | -3.9074 | -16.7138 | 53.2278 | 4 | 3.6009 | 0.2624 | -2.4159 | 0.0191 | -0.1759 | 1.6209 | -0.0064 | -0.5575 | 0.0696 | 0.5324 | 0.0086 | 0.1309 | -0.4117 | 0.371 | 0.0147 | 0.3284 | -0.0008 | 0.0396 | 0.155 | 0.029 | 0.0864 | -9.7442 | -27.0467 | 67.5762 | 5 | 1.0474 | 0.403 | -0.4328 | 1.0324 | -0.6841 | 2.4104 | -0.0537 | -0.0747 | -0.034 | 0.2101 | -0.0915 | 0.0004 | -0.1031 | 0.1778 | -0.0168 | 0.2751 | 0.0148 | 0.0824 | 0.0902 | 0.0236 | 0.0406 | -13.3551 | -29.3019 | 63.8766 | 6 | 0.1446 | -0.2853 | 0.2866 | 0.7908 | -0.8519 | 1.1816 | -0.0426 | 0.0329 | 0.0695 | 0.2426 | 0.1083 | 0.1728 | -0.1818 | -0.1218 | -0.1311 | 0.2408 | -0.0182 | 0.0767 | 0.0901 | 0.0375 | 0.045 | -17.4465 | -24.1837 | 60.4066 | 7 | 1.6252 | 0.278 | 0.8816 | 3.5241 | 1.6544 | 3.3829 | 0.1212 | -0.3291 | -0.2197 | 0.2771 | -0.0679 | 0.1493 | 0.193 | -0.1695 | -0.0254 | 0.1282 | 0.0004 | 0.029 | 0.1007 | 0.0349 | 0.0816 | -20.6902 | -52.3632 | 74.7374 | 8 | 4.4898 | 0.88 | 1.7873 | 2.3576 | 0.7218 | 3.4505 | 0.1117 | 0.2219 | -0.2207 | -0.0193 | -0.0049 | -0.6579 | -0.0448 | 0.7812 | -0.0412 | 0.1867 | -0.0204 | 0.0894 | 0.2507 | 0.0722 | 0.2344 | -6.5101 | -47.9908 | 68.5415 | 9 | 0.1135 | 0.0769 | 0.2164 | 0.2 | 0.2896 | 0.551 | -0.0271 | 0.1268 | 0.1395 | -0.1707 | -0.0921 | -0.5192 | -0.1978 | 0.5672 | -0.11 | 0.2296 | -0.0524 | 0.0985 | 0.3582 | 0.1643 | 0.4258 | -3.0895 | -40.2893 | 67.589 | 10 | 2.4859 | 2.6277 | 1.1504 | 3.9559 | -0.2047 | 3.0432 | -0.0389 | 0.3036 | -0.1546 | -0.247 | 0.1512 | -0.052 | 0.2661 | 0.3142 | -0.0614 | 0.1655 | 0.0438 | 0.0879 | 0.1188 | 0.0185 | 0.0895 | -16.0822 | -52.595 | 63.6095 | 11 | 5.5414 | 1.5865 | 3.0204 | 1.7241 | 1.1198 | 5.0083 | 0.317 | -0.296 | -0.3622 | 0.0785 | -0.1462 | -0.3703 | -0.0059 | 0.2074 | -0.1151 | 0.1683 | -0.0174 | 0.0421 | 0.1309 | 0.0883 | 0.1572 | -11.793 | -47.0612 | 72.3125 | 12 | 1.2631 | 0.4533 | -0.2839 | 1.3102 | -1.1238 | 0.9953 | 0.106 | -0.3701 | 0.2326 | 0.2959 | -0.1756 | -0.0073 | -0.2372 | 0.2629 | 0.0428 | 0.2184 | 0.0047 | -0.073 | 0.1809 | -0.067 | 0.1251 | -29.8994 | -70.8603 | 77.8941 | 13 | 1.2648 | 0.1212 | 0.1031 | 2.1883 | -0.4392 | 1.4234 | -0.0055 | -0.1191 | -0.0472 | 0.0826 | 0.0525 | 0.579 | 0.029 | -0.5619 | -0.019 | 0.118 | -0.0003 | -0.0318 | 0.2495 | -0.064 | 0.191 | -43.7585 | -77.6198 | 74.2871 | 14 | 2.8438 | 3.5902 | -0.996 | 4.5472 | -1.034 | 3.661 | -0.1113 | 0.1599 | 0.3876 | -0.2439 | 0.1011 | 0.5484 | -0.1908 | -0.4857 | 0.065 | 0.1941 | 0.0311 | -0.136 | 0.1744 | -0.0464 | 0.2015 | -41.6075 | -70.4814 | 66.36 | 15 | 4.0135 | 0.5504 | 1.1965 | 3.5813 | 0.1173 | 3.6727 | -0.1663 | 0.2865 | -0.6413 | -0.1792 | -0.0247 | 0.9642 | 0.747 | -0.8967 | 0.1883 | 0.3555 | -0.1098 | -0.0543 | 0.2925 | -0.0576 | 0.3703 | -46.2154 | -83.2239 | 70.6955 | 16 | 3.3397 | 2.3293 | -1.4771 | 3.8526 | -0.7974 | 3.5829 | 0.1786 | 0.0828 | 0.2087 | -0.1953 | -0.231 | 0.0439 | -0.3531 | -0.1271 | 0.0129 | 0.1585 | 0.0332 | -0.0848 | 0.0657 | -0.0086 | 0.073 | -33.2945 | -70.6169 | 66.5198 | 17 | 3.1451 | 0.8866 | -2.6171 | 1.4193 | -1.401 | 4.2719 | 0.0539 | -0.193 | -0.054 | -0.0763 | -0.0888 | 0.3367 | -0.0559 | -0.0835 | 0.09 | 0.1459 | 0.0164 | -0.0298 | 0.0674 | -0.0788 | 0.2025 | -36.6042 | -75.8397 | 74.5677 | 18 | 5.3839 | -2.1734 | 0.5627 | 5.7721 | -0.0868 | 3.3769 | 0.0744 | 0.3428 | 0.1891 | -0.1 | -0.149 | -0.6596 | -0.162 | 0.6174 | 0.0677 | 0.1903 | -0.0218 | -0.0212 | 0.1998 | 0.0097 | 0.1332 | -21.8096 | -77.4227 | 47.0864 | 19 | 2.2852 | -0.1069 | 1.5339 | 0.1155 | -0.0366 | 1.8095 | 0.0132 | 0.0783 | -0.0277 | -0.0235 | -0.0529 | 0.0142 | 0.0489 | -0.0542 | -0.0188 | 0.2496 | 0.0171 | -0.1121 | 0.1016 | -0.0266 | 0.0757 | -36.2769 | -81.5287 | 48.0289 | 20 | 6.5905 | 2.5805 | 7.1488 | 3.5422 | 2.1156 | 8.8139 | -0.1607 | -0.9824 | 0.1203 | 0.4565 | -0.1231 | 0.3676 | -0.1119 | -1.0423 | 0.2375 | 0.1769 | 0.0261 | -0.0297 | 0.2951 | -0.0023 | 0.1826 | -42.5188 | -77.8225 | 53.5639 | 21 | 2.6444 | -1.6367 | -1.0091 | 4.439 | 0.089 | 2.9529 | 0.0882 | 0.0409 | -0.1395 | -0.2559 | 0.0439 | -0.2767 | 0.3357 | 0.272 | -0.074 | 0.2108 | 0.0284 | -0.0419 | 0.0431 | -0.0407 | 0.127 | -27.0949 | -87.2637 | 50.6751 | 22 | 0.6528 | -0.1031 | 0.4565 | 1.6377 | -0.324 | 1.4013 | -0.1481 | 0.1953 | 0.1563 | 0.1174 | -0.0711 | -0.1096 | -0.0393 | 0.0696 | -0.0527 | 0.2377 | 0.0089 | -0.1011 | 0.1333 | -0.0534 | 0.0996 | -31.2732 | -77.2849 | 49.3776 | 23 | 0.1104 | 0.1057 | -0.4258 | 0.275 | -0.3092 | 1.7008 | -0.0243 | -0.098 | 0.0429 | 0.2942 | 0.0819 | -0.2915 | -0.0298 | 0.2275 | -0.1759 | 0.3356 | 0.0596 | -0.1821 | 0.0878 | -0.1051 | 0.1704 | -22.4507 | -99.4954 | 69.2678 | 24 | 1.5223 | 0.6322 | 2.2664 | 1.2708 | 1.7597 | 4.6467 | -0.0451 | -0.1154 | 0.1127 | 0.2891 | 0.0724 | -0.2148 | 0.0432 | 0.0395 | -0.1239 | 0.2175 | 0.0255 | -0.1188 | 0.056 | -0.0289 | 0.1031 | -26.9276 | -89.6408 | 69.9834 | 25 | 0.2691 | -0.1914 | 0.817 | 3.5868 | 2.9183 | 6.0329 | 0.0335 | 0.11 | -0.1214 | 0.217 | -0.0409 | 0.0895 | 0.4157 | -0.4535 | -0.0302 | 0.1596 | -0.0152 | 0.0105 | 0.1188 | -0.0418 | 0.0067 | -43.6646 | -105.0706 | 56.2957 | 26 | 2.0104 | -0.383 | 1.7575 | 0.6718 | -0.2982 | 1.5387 | -0.0076 | -0.5365 | -0.0283 | 0.5656 | -0.009 | 0.0082 | 0.0684 | -0.6744 | 0.0339 | 0.3259 | -0.0094 | 0.0425 | 0.1744 | -0.0017 | 0.0529 | -39.6513 | -96.2868 | 71.2807 | 27 | 0.5179 | 0.2937 | -0.174 | 0.8174 | 0.4751 | 1.0303 | -0.0902 | 0.0004 | 0.0598 | 0.1569 | -0.0002 | -0.0403 | -0.0241 | -0.1447 | -0.049 | 0.2943 | 0.0566 | -0.0733 | 0.1164 | -0.0292 | 0.0554 | -36.4507 | -91.9222 | 65.0346 | 28 | 3.025 | -1.1277 | 2.6689 | 2.3469 | 2.4706 | 8.5891 | 0.1727 | -0.38 | -0.0665 | 0.5003 | -0.3421 | 0.2446 | 0.76 | -0.5805 | 0.1509 | 0.3556 | -0.0444 | -0.0278 | 0.1332 | -0.0162 | 0.1019 | -34.3722 | -99.7104 | 72.3232 | 29 | 0.1944 | -0.0833 | 0.0853 | 0.3858 | 0.5344 | 1.2119 | -0.0476 | 0.0027 | 0.0036 | 0.186 | 0.1317 | -0.1351 | 0.0387 | 0.0953 | 0.0359 | 0.2417 | 0.0409 | -0.0747 | 0.0529 | -0.0872 | 0.0665 | -31.3466 | -98.2251 | 64.3081 | 30 | 2.6972 | -1.3326 | -0.2372 | 4.3273 | -0.3714 | 2.9658 | -0.0131 | 0.2478 | -0.5368 | -0.2704 | -0.0795 | 0.5766 | 0.2211 | -0.5332 | 0.0683 | 0.2231 | -0.0768 | 0.0024 | 0.2124 | -0.0311 | 0.1865 | -27.6116 | -45.7722 | 44.0767 | 31 | 1.958 | 0.0962 | -1.4264 | 0.0345 | 0.0382 | 1.4699 | 0.0383 | -0.0096 | 0.1107 | -0.0964 | -0.077 | -0.1114 | -0.0961 | 0.1007 | -0.04 | 0.2307 | 0.0185 | 0.0683 | 0.0961 | 0.0563 | 0.063 | -13.1644 | -41.7216 | 44.9794 | 32 | 5.2814 | 0.3348 | -0.1495 | 2.52 | -0.5554 | 0.1524 | -0.2999 | -0.1827 | -0.1632 | 0.0988 | 0.1278 | -0.2033 | -0.0398 | 0.3175 | 0.1623 | 0.3048 | -0.0122 | 0.0417 | 0.2535 | 0.015 | 0.1104 | -6.8981 | -45.5281 | 50.3956 | 33 | 4.2795 | -2.1668 | 2.5604 | 4.829 | -0.028 | 2.1098 | -0.0795 | 0.0213 | 0.1348 | -0.1643 | -0.0095 | 0.0921 | -0.5724 | -0.2667 | 0.0139 | 0.2372 | 0.0355 | 0.0382 | 0.1251 | 0.0579 | 0.0921 | -22.3641 | -36.032 | 47.6577 | 34 | 2.5992 | -1.9912 | -1.198 | 4.0034 | 1.3306 | 0.7256 | -0.1955 | 0.2315 | -0.3462 | 0.0436 | -0.0518 | 0.1844 | 0.2285 | -0.2262 | 0.2489 | 0.1648 | 0.0271 | 0.0136 | 0.1557 | 0.0352 | 0.0827 | -19.8534 | -43.9489 | 47.6531 |
|
---|
Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resseq 4:39)A4 - 39 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 40:49)A40 - 49 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 50:61)A50 - 61 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 62:74)A62 - 74 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 75:99)A75 - 99 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 100:121)A100 - 121 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resseq 4:39)B4 - 39 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq 40:74)B40 - 74 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 75:84)B75 - 84 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 85:99)B85 - 99 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 100:121)B100 - 121 | 12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resseq 4:39)C4 - 39 | 13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resseq 40:61)C40 - 61 | 14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resseq 62:74)C62 - 74 | 15 | X-RAY DIFFRACTION | 15 | chain 'C' and ( | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|