Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE)refinementiMOSFLM | | data reductionAimless | | data scalingMOLREP | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BW0 Resolution: 2.75→38.72 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 22.3 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.183 | 1626 | 5 % |
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Rwork | 0.1668 | - | - |
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obs | 0.1677 | 32687 | 98.99 % |
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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: 77.56 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.75→38.72 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 4184 | 24 | 16 | 4224 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 4704 | X-RAY DIFFRACTION | f_angle_d0.575 | 7344 | X-RAY DIFFRACTION | f_dihedral_angle_d11.881 | 2272 | X-RAY DIFFRACTION | f_chiral_restr0.03 | 952 | X-RAY DIFFRACTION | f_plane_restr0.005 | 192 | | | | | |
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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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2.75-2.8309 | 0.4378 | 128 | 0.4205 | 2524 | X-RAY DIFFRACTION | 98 | 2.8309-2.9223 | 0.3911 | 133 | 0.3532 | 2581 | X-RAY DIFFRACTION | 99 | 2.9223-3.0267 | 0.3894 | 130 | 0.3087 | 2538 | X-RAY DIFFRACTION | 99 | 3.0267-3.1478 | 0.2653 | 135 | 0.269 | 2517 | X-RAY DIFFRACTION | 99 | 3.1478-3.291 | 0.2699 | 122 | 0.2228 | 2568 | X-RAY DIFFRACTION | 99 | 3.291-3.4644 | 0.2052 | 114 | 0.2024 | 2582 | X-RAY DIFFRACTION | 99 | 3.4644-3.6813 | 0.1533 | 166 | 0.1462 | 2536 | X-RAY DIFFRACTION | 99 | 3.6813-3.9653 | 0.1598 | 147 | 0.1304 | 2592 | X-RAY DIFFRACTION | 100 | 3.9653-4.3638 | 0.1654 | 164 | 0.1289 | 2580 | X-RAY DIFFRACTION | 100 | 4.3638-4.9941 | 0.1681 | 131 | 0.1314 | 2627 | X-RAY DIFFRACTION | 99 | 4.9941-6.2877 | 0.1381 | 136 | 0.1213 | 2654 | X-RAY DIFFRACTION | 99 | 6.2877-38.7239 | 0.1436 | 120 | 0.1573 | 2762 | X-RAY DIFFRACTION | 98 |
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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 | 0.9546 | 0.4101 | 0.206 | 0.0559 | 0.0105 | 0.0962 | 0.0792 | -0.0957 | 0.4333 | 0.1529 | -0.252 | -0.2838 | -0.4062 | 0.1453 | -0.0002 | 0.5641 | 0.0372 | 0.0096 | 0.5796 | 0.0441 | 0.5895 | -4.5001 | -11.0224 | 20.6486 | 2 | 0.5305 | 0.0373 | -0.0306 | 0.2245 | 0.1535 | 0.0837 | 0.0957 | 1.2962 | 0.2151 | -0.1693 | -0.3381 | -0.7406 | 0.4592 | -1.2989 | -0.0021 | 0.6746 | 0.17 | 0.0895 | 0.9959 | 0.088 | 0.6755 | 4.8964 | -11.7533 | 0.0625 | 3 | 0.2477 | -0.2434 | -0.1178 | 0.1983 | 0.0617 | 0.1218 | 0.6492 | 1.2279 | 0.3708 | -0.4772 | -0.3419 | -0.2456 | 0.4426 | 0.3378 | -0.0007 | 0.6834 | 0.202 | 0.0148 | 1.0705 | 0.0983 | 0.6102 | -2.9794 | -13.8798 | -1.7998 | 4 | 0.5706 | -0.0707 | 0.3491 | 0.2554 | -0.2355 | 0.3287 | 0.7178 | 0.4186 | -0.4786 | -0.701 | -0.2098 | -0.8412 | -0.1434 | -0.7094 | 0.0016 | 0.5899 | 0.0666 | -0.0378 | 0.6053 | 0.1558 | 0.5505 | -10.8773 | -13.4328 | 13.0659 | 5 | 0.194 | -0.0835 | -0.1135 | 0.0203 | 0.0676 | 0.0458 | 0.2865 | 0.1838 | -0.0425 | -0.0234 | -0.0782 | -0.1143 | -0.4798 | 0.5674 | -0.0023 | 0.5173 | -0.0384 | -0.0629 | 0.6371 | 0.0937 | 0.5523 | 1.9531 | -11.7016 | 18.001 | 6 | 0.0957 | -0.1145 | 0.0207 | 0.2626 | -0.1329 | 0.0637 | -0.237 | -0.4798 | -0.2703 | -0.3337 | -0.2767 | 0.6532 | 0.7603 | 0.6085 | -0.0029 | 0.5504 | -0.023 | -0.0076 | 0.629 | -0.0106 | 0.5281 | 2.7605 | -24.7613 | 26.0641 | 7 | 0.9832 | -0.0571 | -0.0434 | 0.8863 | 0.5896 | 0.3211 | 0.331 | 0.6863 | -0.3477 | 0.1048 | -0.3505 | 0.1485 | 0.8825 | 0.0619 | -0.0011 | 0.598 | 0.1512 | -0.0418 | 0.7242 | -0.0222 | 0.6274 | -1.2994 | -32.3005 | 11.071 | 8 | 0.1985 | 0.2036 | -0.1848 | 0.2741 | -0.1873 | 0.1347 | 0.331 | 2.7485 | -0.544 | -0.3105 | -0.0711 | 0.6203 | 0.2612 | 0.6751 | -0 | 0.6493 | 0.1491 | -0.0574 | 1.2948 | -0.1277 | 0.664 | -4.3986 | -30.7032 | -4.7142 | 9 | 0.3181 | -0.0478 | -0.1666 | 0.5429 | 0.4459 | 0.4069 | 0.2355 | 0.365 | -0.1444 | -0.1891 | 0.4961 | 0.0776 | 0.0319 | 0.4914 | 0.0003 | 0.6086 | 0.1134 | 0.0105 | 0.6898 | 0.0072 | 0.5786 | 6.8594 | -27.0009 | 8.7938 | 10 | 0.2356 | 0.1537 | 0.3236 | 0.4099 | 0.4368 | 0.561 | -0.3292 | 0.0796 | 0.0146 | 0.1448 | 0.1021 | -0.0884 | 0.8673 | -0.0032 | 0.0009 | 0.5614 | -0.0209 | 0.0714 | 0.582 | -0.0935 | 0.616 | -1.3191 | -28.3009 | 18.8185 | 11 | 1.0195 | 0.3449 | 0.1088 | 0.5097 | 0.7471 | 1.151 | -0.3486 | 1.3252 | -1.0663 | 0.8312 | 1.7427 | -0.6632 | 0.4056 | 0.9414 | 0.0445 | 0.808 | -0.0704 | 0.2236 | 0.6995 | 0.0354 | 1.1718 | 16.3274 | -47.2998 | 6.274 | 12 | 0.7647 | 0.0192 | 0.1357 | 0.3667 | 0.6005 | 0.9038 | -0.0077 | -0.7242 | 0.0624 | 0.3158 | -0.0121 | -0.258 | 0.6413 | 0.6526 | -0.0011 | 0.6158 | 0.1247 | 0.1075 | 0.8185 | 0.1651 | 0.8217 | 19.363 | -33.4409 | 12.9805 | 13 | 0.3006 | -0.094 | 0.1349 | 0.0942 | -0.0381 | 0.3769 | 0.2271 | -0.5038 | 0.771 | 0.6831 | -0.5151 | 0.3937 | -0.1971 | 1.0857 | -0.0029 | 0.6885 | -0.079 | 0.1013 | 0.8196 | -0.0031 | 0.9155 | 26.0174 | -16.932 | 9.3674 | 14 | 1.1321 | -0.6281 | -0.075 | 0.4055 | 0.0749 | 0.0706 | 0.3793 | -0.3422 | 0.4567 | -0.1141 | -0.4012 | -0.0444 | -0.0041 | 0.6521 | 0.0001 | 0.6156 | 0.0205 | 0.0952 | 0.6581 | 0.0334 | 0.7434 | 15.2293 | -25.7949 | 7.6978 | 15 | 0.3457 | 0.3515 | -0.4435 | 1.3707 | 0.5091 | 1.2198 | -0.243 | 0.1313 | -0.6281 | 0.3073 | -0.1351 | -0.2934 | 0.2878 | 0.2583 | 0.0003 | 0.5892 | 0.1876 | 0.0314 | 0.639 | -0.0346 | 0.8157 | 18.011 | -38.8735 | 8.2216 | 16 | 0.2968 | -0.1972 | 0.1124 | 0.3065 | -0.2255 | 0.4887 | 0.2006 | 0.685 | 0.7576 | 2.5713 | -0.1615 | -1.0001 | 0.7405 | 1.1745 | -0.0326 | 1.3282 | -0.0877 | -0.418 | 1.3034 | -0.2864 | 1.2314 | 24.2224 | -1.2928 | 55.1871 | 17 | 0.0964 | 0.1748 | -0.1261 | 0.2369 | -0.0798 | 0.4293 | -0.3361 | 0.2749 | 0.6317 | -0.629 | 0.5973 | -0.4098 | 0.2053 | 1.3382 | 0.0014 | 0.755 | 0.0294 | -0.1084 | 0.926 | -0.2612 | 1.0209 | 17.4935 | -4.1091 | 41.4041 | 18 | 0.1355 | -0.0241 | -0.1317 | 0.3563 | -0.0039 | 0.1702 | -0.4351 | 0.5798 | -0.3411 | 0.33 | 0.2886 | -0.045 | -0.2287 | 0.3148 | -0.0006 | 0.7551 | 0.0229 | -0.1251 | 0.5497 | 0.0178 | 0.6001 | 2.4507 | -10.4825 | 33.9526 | 19 | 0.3496 | -0.7183 | 0.4166 | 1.9196 | -0.5198 | 0.2633 | -0.081 | -0.2125 | -0.3873 | 0.1049 | 0.5444 | 0.0503 | -0.1482 | 0.5145 | 0.0003 | 0.7253 | -0.0124 | -0.1157 | 0.7408 | -0.1645 | 0.6333 | 10.5018 | 2.0452 | 43.2314 | 20 | 0.0971 | 0.1251 | 0.0638 | 0.3078 | 0.0449 | 0.0458 | 0.3684 | -0.1685 | -0.4159 | 0.7349 | 0.3741 | -0.6031 | 0.6022 | 1.8027 | 0.0002 | 1.0136 | 0.2432 | -0.3179 | 0.9944 | -0.2558 | 0.9715 | 20.4457 | -7.7857 | 48.06 | 21 | 0.2493 | -0.3677 | 0.4875 | 0.6402 | -0.7589 | 0.9185 | -0.6481 | 0.5638 | 0.3253 | 0.3522 | 1.0808 | -0.7412 | -1.5739 | -0.087 | -0.0014 | 0.919 | -0.2014 | -0.1814 | 0.7344 | -0.0291 | 1.079 | -18.0196 | 5.5333 | 3.3962 | 22 | 0.6146 | 0.0355 | -0.0197 | 0.2593 | -0.4528 | 0.6403 | 0.0657 | -0.714 | -0.1692 | 0.7029 | -0.1515 | 0.1185 | -0.7271 | -0.7234 | -0.0004 | 0.6623 | 0.125 | -0.0881 | 0.7839 | -0.0799 | 0.788 | -21.1189 | -7.3043 | 11.6169 | 23 | 0.3804 | -0.0206 | 0.1936 | 0.1821 | 0.1986 | 0.3049 | 0.3916 | -0.519 | -0.128 | 0.7119 | -0.6316 | -0.3673 | 0.249 | -1.1227 | -0.0016 | 0.7117 | -0.2008 | -0.1013 | 0.9862 | 0.167 | 0.8281 | -27.9165 | -24.0434 | 9.8743 | 24 | 2.2114 | -1.595 | 0.6425 | 1.2217 | -0.1029 | 0.7552 | 0.6798 | 0.025 | -0.7056 | -0.1692 | -0.7321 | -0.0998 | -0.0448 | -0.3966 | 0 | 0.6335 | 0.006 | -0.1144 | 0.611 | 0.1075 | 0.6137 | -15.5086 | -14.0193 | 6.3572 | 25 | -0.0091 | -0.0446 | -0.0137 | 0.2427 | -0.1981 | 0.6279 | 0.2368 | 0.1186 | 0.7372 | 0.178 | -0.248 | 0.0712 | -1.0042 | -0.2354 | 0.0002 | 0.6795 | 0.1734 | 0.0341 | 0.7109 | 0.1032 | 0.8473 | -22.2823 | -1.6116 | 7.0428 | 26 | 0.1795 | 0.0025 | 0.016 | 0.0047 | -0.0037 | -0.0073 | 0.706 | 0.4492 | -0.3011 | -1.86 | -0.5227 | -0.7782 | -0.2769 | 0.6326 | 0.0058 | 1.2127 | 0.0179 | 0.4077 | 1.1972 | -0.2919 | 1.0313 | 21.1659 | 11.8872 | 28.2015 | 27 | 0.0011 | -0.0266 | 0.0168 | 0.2366 | 0.0207 | 0.0189 | -0.6009 | 1.2624 | -1.4547 | 0.9956 | -0.0782 | 0.1835 | 0.0447 | 0.1627 | -0.0076 | 0.8253 | -0.1548 | 0.2988 | 0.8284 | -0.2066 | 0.9199 | 15.9369 | 16.6372 | 42.3765 | 28 | 0.2287 | 0.1522 | 0.0079 | 0.2566 | -0.1451 | 0.1783 | -0.2374 | 0.4822 | -0.0855 | -0.8521 | -0.1947 | 0.4843 | 0.4873 | -0.2257 | -0.0006 | 0.6718 | -0.1112 | 0.0759 | 0.5468 | -0.0542 | 0.5281 | 5.591 | 22.0223 | 52.449 | 29 | 0.2632 | -0.3441 | 0.0259 | 0.8044 | -0.4772 | 0.4874 | 0.0343 | 0.3279 | 0.33 | -0.1843 | 0.6189 | -0.28 | 0.2667 | 0.3904 | -0 | 0.7164 | -0.0818 | 0.0984 | 0.7225 | -0.1707 | 0.5546 | 9.2597 | 9.6069 | 42.5184 | 30 | 0.5172 | 0.0219 | 0.4286 | 0.2843 | 0.1569 | 0.5324 | 0.5258 | 0.4346 | -0.1142 | -0.9007 | -0.107 | -0.7435 | -0.1225 | 0.3808 | 0.0023 | 1.1073 | -0.2751 | 0.241 | 0.808 | -0.1892 | 0.7581 | 17.4814 | 16.462 | 33.2855 | 31 | 0.1005 | 0.0686 | -0.0151 | 0.0627 | 0.0055 | -0.0042 | 0.921 | 0.0268 | -0.0253 | 0.2381 | -0.3654 | -0.6557 | -0.3482 | 1.1133 | 0.0048 | 1.6024 | 0.2145 | -0.4504 | 1.3001 | -0.0775 | 1.2218 | 18.5718 | -9.174 | 62.8339 | 32 | -0.0017 | 0.0121 | 0.0244 | 0.2746 | 0.0685 | 0.0322 | -0.0806 | -0.8648 | 0.2882 | 0.541 | 0.4102 | 0.4283 | -0.0659 | 1.184 | -0.0038 | 1.5026 | -0.0253 | -0.1075 | 0.8986 | -0.0791 | 0.8138 | 4.2579 | -7.6764 | 62.8214 | 33 | 0.1616 | -0.057 | -0.0386 | 0.0427 | 0.0103 | 0.0109 | 1.1286 | -0.4681 | -2.1866 | 0.3377 | 0.6931 | 0.7095 | -0.6524 | -0.1753 | 0.008 | 1.1978 | 0.0765 | -0.0669 | 0.6972 | -0.0291 | 1.0807 | -5.9083 | 1.4513 | 50.6838 | 34 | 0.3142 | 0.4216 | 0.1349 | 0.7662 | -0.0036 | 0.0476 | -0.1315 | 0.1568 | 0.0836 | 0.3594 | 0.4226 | 0.6445 | 0.0326 | 0.2907 | 0.0013 | 1.0655 | 0.0443 | -0.0392 | 0.8145 | 0.041 | 0.8706 | -1.85 | -9.3355 | 51.7477 | 35 | 0.7183 | -0.3116 | -0.3626 | 0.2029 | 0.062 | 0.2582 | 0.0214 | -0.6396 | -0.0804 | 1.0991 | 0.784 | -0.7797 | 0.2851 | 0.5497 | -0.0006 | 1.2366 | -0.012 | -0.1839 | 1.0459 | -0.2612 | 1.0903 | 10.5526 | -7.6356 | 60.0682 | 36 | 0.9087 | 0.843 | 0.4689 | 1.2207 | 0.1821 | 0.3266 | 0.1806 | -0.8053 | -0.4214 | 0.7042 | 0.305 | -0.5142 | 0.1203 | -0.2629 | 0.0002 | 1.4968 | -0.0149 | 0.0912 | 0.9188 | 0.0597 | 0.8705 | 1.9478 | -26.3021 | 60.5434 | 37 | 0.0849 | -0.0431 | 0.1365 | 0.0771 | -0.1214 | 0.15 | -0.4156 | -0.2385 | -0.4491 | 0.4413 | 1.2289 | -1.3936 | -0.0307 | 0.3353 | -0.0017 | 1.0828 | -0.029 | 0.1533 | 0.7174 | -0.0752 | 1.2378 | 10.5027 | -30.0706 | 44.8581 | 38 | 0.542 | 0.2891 | 0.1157 | 0.267 | 0.1277 | 0.1894 | -0.3076 | -0.2814 | 0.6503 | 0.641 | 1.0148 | -0.2867 | 0.3437 | -0.4094 | 0.0007 | 1.1428 | 0.0154 | 0.1033 | 0.8314 | 0.0047 | 0.7914 | 0.149 | -18.7573 | 54.1815 | 39 | 0.4023 | -0.1189 | -0.0428 | 0.0621 | -0.0291 | 0.0504 | 0.5568 | -1.2491 | 0.2989 | 0.4456 | -0.3223 | -0.4617 | -0.1279 | -0.097 | 0.0003 | 1.335 | 0.1116 | 0.1232 | 0.9632 | 0.2272 | 1.0226 | -3.2456 | -25.5253 | 62.508 |
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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 1:7)2 | X-RAY DIFFRACTION | 2 | (CHAIN A AND RESID 8:12)3 | X-RAY DIFFRACTION | 3 | (CHAIN A AND RESID 13:16)4 | X-RAY DIFFRACTION | 4 | (CHAIN A AND RESID 17:20)5 | X-RAY DIFFRACTION | 5 | (CHAIN A AND RESID 21:24)6 | X-RAY DIFFRACTION | 6 | (CHAIN B AND RESID 1:4)7 | X-RAY DIFFRACTION | 7 | (CHAIN B AND RESID 5:10)8 | X-RAY DIFFRACTION | 8 | (CHAIN B AND RESID 11:14)9 | X-RAY DIFFRACTION | 9 | (CHAIN B AND RESID 15:19)10 | X-RAY DIFFRACTION | 10 | (CHAIN B AND RESID 20:24)11 | X-RAY DIFFRACTION | 11 | (CHAIN C AND RESID 1:4)12 | X-RAY DIFFRACTION | 12 | (CHAIN C AND RESID 5:9)13 | X-RAY DIFFRACTION | 13 | (CHAIN C AND RESID 10:13)14 | X-RAY DIFFRACTION | 14 | (CHAIN C AND RESID 14:18)15 | X-RAY DIFFRACTION | 15 | (CHAIN C AND RESID 19:24)16 | X-RAY DIFFRACTION | 16 | (CHAIN D AND RESID 1:4)17 | X-RAY DIFFRACTION | 17 | (CHAIN D AND RESID 5:9)18 | X-RAY DIFFRACTION | 18 | (CHAIN D AND | | | | | | | | | | | | | | | | | |
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