Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE: DEV_1769)refinementXDS | | data reductionPDB_EXTRACT | 3.15 | data extractionXSCALE | | data scalingBALBES | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UVD Resolution: 1.85→37.46 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.3 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.19 | 3750 | 4.66 % |
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Rwork | 0.154 | - | - |
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obs | 0.156 | 80438 | 94.1 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 21.13 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.85→37.46 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6889 | 0 | 47 | 750 | 7686 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 7049 | X-RAY DIFFRACTION | f_angle_d0.961 | 9572 | X-RAY DIFFRACTION | f_dihedral_angle_d11.92 | 2444 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 1154 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1261 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Number | Refine-ID | Type |
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1 | 1 | A4171 | X-RAY DIFFRACTION | POSITIONAL1 | 2 | B4171 | X-RAY DIFFRACTION | POSITIONAL1 | 3 | C4171 | X-RAY DIFFRACTION | POSITIONAL1 | 4 | D4171 | X-RAY DIFFRACTION | POSITIONAL | | | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.85-1.8735 | 0.2607 | 113 | 0.1962 | 2521 | X-RAY DIFFRACTION | 85 | 1.8735-1.8981 | 0.2568 | 164 | 0.2072 | 2567 | X-RAY DIFFRACTION | 86 | 1.8981-1.9241 | 0.2256 | 127 | 0.1896 | 2584 | X-RAY DIFFRACTION | 87 | 1.9241-1.9516 | 0.2545 | 148 | 0.1873 | 2651 | X-RAY DIFFRACTION | 89 | 1.9516-1.9807 | 0.2131 | 127 | 0.1814 | 2668 | X-RAY DIFFRACTION | 89 | 1.9807-2.0117 | 0.2306 | 132 | 0.1714 | 2737 | X-RAY DIFFRACTION | 90 | 2.0117-2.0447 | 0.2005 | 130 | 0.1657 | 2727 | X-RAY DIFFRACTION | 92 | 2.0447-2.0799 | 0.1914 | 92 | 0.1635 | 2812 | X-RAY DIFFRACTION | 92 | 2.0799-2.1178 | 0.202 | 125 | 0.1622 | 2809 | X-RAY DIFFRACTION | 93 | 2.1178-2.1585 | 0.1963 | 137 | 0.1605 | 2813 | X-RAY DIFFRACTION | 94 | 2.1585-2.2025 | 0.2114 | 129 | 0.1501 | 2859 | X-RAY DIFFRACTION | 94 | 2.2025-2.2504 | 0.2154 | 112 | 0.1518 | 2895 | X-RAY DIFFRACTION | 95 | 2.2504-2.3028 | 0.1942 | 133 | 0.1472 | 2846 | X-RAY DIFFRACTION | 95 | 2.3028-2.3603 | 0.1764 | 138 | 0.1509 | 2870 | X-RAY DIFFRACTION | 95 | 2.3603-2.4241 | 0.2104 | 113 | 0.1528 | 2893 | X-RAY DIFFRACTION | 96 | 2.4241-2.4955 | 0.2154 | 147 | 0.1477 | 2883 | X-RAY DIFFRACTION | 95 | 2.4955-2.576 | 0.1831 | 140 | 0.15 | 2899 | X-RAY DIFFRACTION | 97 | 2.576-2.668 | 0.1813 | 135 | 0.1492 | 2949 | X-RAY DIFFRACTION | 97 | 2.668-2.7748 | 0.1884 | 141 | 0.1581 | 2950 | X-RAY DIFFRACTION | 97 | 2.7748-2.9011 | 0.2026 | 147 | 0.1568 | 2909 | X-RAY DIFFRACTION | 98 | 2.9011-3.054 | 0.214 | 152 | 0.1535 | 2989 | X-RAY DIFFRACTION | 98 | 3.054-3.2452 | 0.165 | 131 | 0.1528 | 2943 | X-RAY DIFFRACTION | 98 | 3.2452-3.4956 | 0.1761 | 186 | 0.1457 | 2956 | X-RAY DIFFRACTION | 98 | 3.4956-3.8471 | 0.1727 | 175 | 0.133 | 2989 | X-RAY DIFFRACTION | 99 | 3.8471-4.403 | 0.1773 | 144 | 0.1361 | 2984 | X-RAY DIFFRACTION | 98 | 4.403-5.5444 | 0.1665 | 170 | 0.1419 | 2985 | X-RAY DIFFRACTION | 99 | 5.5444-37.47 | 0.1649 | 162 | 0.1706 | 3000 | X-RAY DIFFRACTION | 97 |
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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) |
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1 | 1.7595 | 0.3159 | 0.4397 | 3.1087 | -0.4889 | 3.1765 | -0.1071 | -0.1338 | 0.3806 | 0.0387 | 0.0565 | 0.1706 | -0.1993 | -0.2728 | 0.0216 | 0.1657 | 0.0632 | -0.0374 | 0.1427 | -0.0433 | 0.2334 | 9.8127 | 25.8159 | 17.3389 | 2 | 1.1664 | -0.1997 | -0.1865 | 4.228 | -0.4102 | 1.4515 | 0.086 | -0.0372 | 0.1833 | 0.4378 | -0.0259 | 0.6734 | -0.2829 | -0.3759 | 0.1946 | 0.3535 | 0.1764 | -0.0426 | 0.3913 | -0.2155 | 0.4926 | 3.1889 | 31.5585 | 23.0724 | 3 | 3.6061 | 3.953 | 0.1121 | 8.0256 | 0.5444 | 0.8449 | -0.0068 | -0.2301 | 0.5202 | -0.4473 | -0.1349 | 0.7373 | -0.1958 | -0.193 | 0.0869 | 0.2007 | 0.0909 | -0.0354 | 0.2549 | -0.0288 | 0.292 | 1.1036 | 23.5836 | 15.6087 | 4 | 1.1198 | -0.1554 | -0.0842 | 1.1262 | -0.2673 | 0.9544 | -0.1064 | -0.1132 | 0.1445 | 0.1138 | 0.0427 | 0.2005 | -0.1655 | -0.2657 | 0.0428 | 0.1322 | 0.0325 | -0.0126 | 0.1918 | -0.0501 | 0.1993 | 3.6216 | 14.2948 | 17.2148 | 5 | 0.6295 | 0.7853 | -0.7195 | 3.9224 | -3.5251 | 5.2853 | 0.0269 | -0.017 | 0.0407 | 0.0473 | -0.0021 | 0.2381 | -0.1841 | -0.2265 | -0.0403 | 0.0827 | 0.0262 | -0.0222 | 0.1855 | -0.0248 | 0.2063 | 4.5614 | 8.8528 | 13.0546 | 6 | 0.557 | 0.0603 | 0.2909 | 1.5275 | -1.4024 | 4.4302 | 0.0187 | -0.0202 | 0.0128 | 0.0798 | -0.0023 | 0.1128 | -0.1015 | -0.0229 | -0.0251 | 0.0506 | 0.0066 | 0.0035 | 0.0963 | -0.0028 | 0.1063 | 14.3861 | 6.7755 | 17.8634 | 7 | 1.2332 | 0.3757 | 1.1509 | 1.2096 | 0.2531 | 1.8132 | 0.0652 | -0.1516 | 0.0705 | 0.134 | -0.0683 | 0.1175 | -0.0122 | -0.2563 | -0.0249 | 0.112 | 0.002 | 0.0093 | 0.1371 | -0.0222 | 0.1308 | 19.2774 | 14.7179 | 24.0973 | 8 | 1.7638 | 0.1103 | 0.5487 | 0.7371 | -0.2297 | 8.462 | 0.018 | -0.0401 | 0.0345 | 0.0674 | -0.0057 | -0.0183 | -0.0092 | -0.1507 | -0.0495 | 0.0724 | -0.0122 | -0.0112 | 0.0764 | -0.0212 | 0.1156 | 24.5171 | 11.1526 | 18.2872 | 9 | 1.7928 | -0.0579 | -1.0845 | 3.5991 | -0.4149 | 2.0691 | 0.0359 | 0.0817 | -0.5489 | 0.0356 | 0.013 | 0.1787 | 0.3653 | -0.288 | -0.0518 | 0.2238 | -0.0977 | -0.0073 | 0.1656 | 0.0003 | 0.2743 | 9.9261 | -25.8643 | 18.4081 | 10 | 2.2447 | -2.1037 | -0.9975 | 2.3018 | 0.3874 | 1.3554 | 0.1597 | 0.2469 | -0.7548 | -0.8362 | 0.0819 | 0.7351 | 0.509 | -0.5831 | -0.1476 | 0.4621 | -0.2226 | -0.0463 | 0.3723 | -0.076 | 0.4959 | 4.2726 | -31.8615 | 12.0515 | 11 | 2.8373 | -2.2758 | 0.386 | 2.2625 | 0.2213 | 1.3504 | -0.1644 | -0.0135 | -0.6672 | 0.4119 | 0.1183 | 0.8018 | 0.3667 | -0.5414 | 0.0334 | 0.2618 | -0.1436 | 0.062 | 0.363 | -0.0217 | 0.3601 | 1.0667 | -23.7148 | 19.329 | 12 | 1.1227 | 0.4658 | 0.0411 | 1.1889 | -0.0628 | 0.5546 | -0.0479 | -0.0649 | -0.2062 | -0.0603 | 0.0396 | 0.2036 | 0.2808 | -0.4431 | -0.0089 | 0.1737 | -0.0718 | 0.0312 | 0.2534 | -0.0227 | 0.245 | 3.6387 | -14.4029 | 17.9797 | 13 | 1.7001 | -1.1503 | 0.9773 | 4.1748 | -3.2942 | 4.5867 | 0.0437 | -0.1386 | -0.1077 | 0.1487 | 0.0314 | 0.3806 | 0.0572 | -0.2852 | -0.1095 | 0.1145 | -0.0528 | 0.0195 | 0.2172 | -0.015 | 0.1977 | 4.0165 | -8.8575 | 21.8938 | 14 | 1.2525 | 0.7287 | -1.2799 | 3.8512 | -3.9049 | 6.9091 | -0.0227 | -0.0613 | -0.0641 | -0.085 | -0.0809 | -0.0168 | 0.2511 | -0.0053 | 0.1341 | 0.0977 | -0.0028 | 0.0009 | 0.1041 | -0.0118 | 0.1036 | 15.7235 | -8.5889 | 15.7502 | 15 | 1.5354 | -0.8267 | -0.1945 | 1.7827 | -0.4314 | 0.943 | -0.0011 | -0.1625 | -0.0601 | 0.1009 | 0.0493 | 0.1915 | 0.1446 | -0.0338 | -0.0556 | 0.0886 | -0.0338 | 0.0125 | 0.1038 | -0.0023 | 0.1218 | 14.587 | -7.771 | 23.3467 | 16 | 4.6687 | -4.085 | 1.7976 | 4.9765 | -3.2487 | 5.6099 | 0.4508 | 0.6132 | 0.0038 | -0.5824 | -0.3105 | 0.4046 | 0.0758 | -1.2359 | -0.0456 | 0.3072 | 0.0653 | -0.042 | 0.4204 | -0.0928 | 0.2168 | 17.7378 | -10.0928 | -0.5362 | 17 | 1.616 | -0.0119 | -0.8675 | 1.1277 | 0.1296 | 5.1478 | 0.0215 | 0.0287 | -0.0673 | -0.0493 | -0.0023 | 0.0517 | 0.1998 | -0.2217 | -0.0182 | 0.0754 | 0.0078 | -0.0018 | 0.0804 | 0.0007 | 0.1142 | 23.3367 | -15.7184 | 15.0783 | 18 | 2.0164 | -0.5949 | 0.2172 | 1.4404 | -0.7146 | 2.2143 | 0.0311 | -0.0418 | -0.0942 | 0.0366 | -0.0102 | -0.0382 | 0.1858 | 0.1315 | -0.0285 | 0.1571 | 0.0348 | 0.0048 | 0.082 | 0.0134 | 0.1017 | 44.0989 | -27.0465 | 25.0461 | 19 | 1.7216 | 2.297 | -0.6032 | 6.3505 | -1.4022 | 1.3649 | -0.079 | 0.0584 | -0.2563 | 0.0327 | -0.0124 | -0.7259 | 0.2277 | 0.2403 | 0.0526 | 0.1873 | 0.0633 | 0.0033 | 0.1485 | 0.0215 | 0.1443 | 51.5562 | -23.4292 | 21.8935 | 20 | 0.7451 | -0.4453 | -0.0692 | 3.0063 | 1.352 | 1.2847 | -0.0051 | 0.0449 | -0.0309 | 0.1129 | 0.0281 | -0.1664 | 0.1633 | 0.1949 | -0.0327 | 0.1137 | 0.0166 | -0.0019 | 0.1391 | 0.0341 | 0.1076 | 48.5379 | -11.9326 | 19.3358 | 21 | 1.2306 | -1.456 | -1.519 | 1.7538 | 2.1752 | 5.276 | -0.0505 | 0.0441 | -0.0439 | 0.189 | -0.1066 | 0.166 | 0.1651 | -0.0456 | 0.157 | 0.0952 | -0.0283 | 0.0016 | 0.1006 | 0.0204 | 0.0999 | 36.562 | -8.7601 | 22.2717 | 22 | 0.7009 | 0.3739 | 0.3118 | 1.1078 | 1.0003 | 1.405 | 0.0203 | 0.0735 | -0.0401 | 0.0265 | -0.0141 | -0.0208 | 0.1242 | 0.0657 | -0.0011 | 0.0987 | 0.014 | -0.0044 | 0.0799 | 0.0125 | 0.0902 | 37.8018 | -8.4558 | 15.2372 | 23 | 5.75 | 3.3317 | 1.7375 | 6.5346 | 1.9814 | 7.3854 | 0.3181 | -0.6337 | 0.4578 | 1.0198 | -0.2578 | -0.3175 | -0.3734 | 0.6554 | -0.089 | 0.4151 | -0.0952 | -0.021 | 0.3666 | -0.003 | 0.2679 | 35.3038 | -7.2821 | 39.8863 | 24 | 1.2391 | -0.606 | -0.5884 | 1.5978 | 0.4299 | 3.265 | -0.0278 | -0.0328 | -0.0311 | 0.1543 | 0.0095 | 0.039 | 0.1218 | -0.036 | 0.0219 | 0.0885 | -0.0211 | -0.0013 | 0.0766 | 0.0133 | 0.1052 | 28.9798 | -14.8345 | 24.362 | 25 | 4.0842 | 0.5259 | 0.701 | 2.1142 | -1.3778 | 3.4923 | 0.0369 | -0.1259 | 0.2908 | 0.1027 | 0.0192 | -0.0591 | -0.2257 | 0.0706 | -0.0881 | 0.1308 | -0.0663 | -0.0229 | 0.0697 | 0.0281 | 0.1055 | 41.6725 | 25.8297 | 18.3658 | 26 | 2.3202 | -0.2259 | -0.5376 | 1.7717 | -0.0632 | 2.761 | -0.0213 | 0.0484 | 0.0837 | 0.0174 | 0.0221 | -0.0499 | -0.1636 | 0.1806 | 0.009 | 0.1666 | -0.041 | -0.0137 | 0.1033 | 0.0142 | 0.1164 | 45.6906 | 27.2058 | 11.6438 | 27 | 3.0015 | -2.6511 | 0.9597 | 7.1105 | -1.6453 | 1.7885 | -0.0771 | -0.071 | 0.1594 | 0.2683 | 0.0499 | -0.5687 | -0.1982 | 0.2416 | 0.0112 | 0.1657 | -0.0718 | -0.0126 | 0.1698 | 0.0152 | 0.1101 | 51.5912 | 23.5169 | 17.4457 | 28 | 1.0056 | 0.3333 | -0.0379 | 2.1967 | 0.1433 | 0.4014 | -0.0109 | -0.0469 | 0.0532 | -0.1438 | -0.0162 | -0.1245 | -0.2107 | 0.1498 | 0.0178 | 0.1329 | -0.0286 | 0.0009 | 0.1479 | 0.0314 | 0.0917 | 48.8069 | 14.2741 | 17.5608 | 29 | 0.707 | -0.1003 | -0.1181 | 1.1461 | 0.6604 | 1.5239 | 0.0258 | -0.0334 | 0.0036 | 0.0212 | -0.0542 | -0.0401 | -0.063 | 0.0407 | 0.0179 | 0.0983 | -0.0102 | -0.006 | 0.0852 | 0.0195 | 0.088 | 41.2372 | 8.83 | 20.9927 | 30 | 7.6346 | 2.4413 | 1.2378 | 6.3281 | -1.1787 | 3.1898 | 0.1313 | 0.6507 | -0.5305 | -0.6788 | -0.2291 | -0.4532 | 0.361 | 0.7268 | -0.0051 | 0.3649 | 0.0698 | -0.004 | 0.311 | 0.0047 | 0.2297 | 37.59 | 7.2989 | -1.9687 | 31 | 1.2551 | 0.4563 | 0.5084 | 1.326 | 0.8747 | 4.6832 | 0.0584 | 0.0759 | 0.0086 | -0.118 | 0.0335 | -0.0453 | -0.147 | -0.0651 | -0.052 | 0.1104 | 0.0053 | -0.0015 | 0.0677 | 0.0112 | 0.1043 | 30.6468 | 18.0425 | 9.8194 | 32 | 2.0136 | 0.2351 | 0.7678 | 0.0879 | -0.346 | 5.4506 | 0.0244 | -0.0535 | -0.0264 | -0.016 | -0.0075 | 0.0272 | -0.0556 | -0.061 | -0.0257 | 0.0745 | 0.0109 | -0.0055 | 0.0574 | 0.0096 | 0.0963 | 27.8707 | 11.0362 | 17.1461 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | CHAIN 'A' AND (RESID 3 THROUGH 40 )2 | X-RAY DIFFRACTION | 2 | CHAIN 'A' AND (RESID 41 THROUGH 54 )3 | X-RAY DIFFRACTION | 3 | CHAIN 'A' AND (RESID 55 THROUGH 67 )4 | X-RAY DIFFRACTION | 4 | CHAIN 'A' AND (RESID 68 THROUGH 104 )5 | X-RAY DIFFRACTION | 5 | CHAIN 'A' AND (RESID 105 THROUGH 133 )6 | X-RAY DIFFRACTION | 6 | CHAIN 'A' AND (RESID 134 THROUGH 173 )7 | X-RAY DIFFRACTION | 7 | CHAIN 'A' AND (RESID 174 THROUGH 240 )8 | X-RAY DIFFRACTION | 8 | CHAIN 'A' AND (RESID 241 THROUGH 258 )9 | X-RAY DIFFRACTION | 9 | CHAIN 'B' AND (RESID 3 THROUGH 40 )10 | X-RAY DIFFRACTION | 10 | CHAIN 'B' AND (RESID 41 THROUGH 54 )11 | X-RAY DIFFRACTION | 11 | CHAIN 'B' AND (RESID 55 THROUGH 67 )12 | X-RAY DIFFRACTION | 12 | CHAIN 'B' AND (RESID 68 THROUGH 104 )13 | X-RAY DIFFRACTION | 13 | CHAIN 'B' AND (RESID 105 THROUGH 133 )14 | X-RAY DIFFRACTION | 14 | CHAIN 'B' AND (RESID 134 THROUGH 153 )15 | X-RAY DIFFRACTION | 15 | CHAIN 'B' AND (RESID 154 THROUGH 186 )16 | X-RAY DIFFRACTION | 16 | CHAIN 'B' | | | | | | | | | | | | | | | |
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