Software | Name | Version | Classification |
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PHENIX | dev_5508refinementAimless | | data scalingXDS | | data reductionPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→47.44 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2273 | 1617 | 5.04 % |
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Rwork | 0.1984 | - | - |
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obs | 0.1998 | 32076 | 99.99 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 2.75→47.44 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5421 | 0 | 10 | 9 | 5440 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.005 | 5516 | X-RAY DIFFRACTION | f_angle_d0.862 | 7398 | X-RAY DIFFRACTION | f_dihedral_angle_d12.485 | 2040 | X-RAY DIFFRACTION | f_chiral_restr0.048 | 826 | X-RAY DIFFRACTION | f_plane_restr0.006 | 961 | | | | | |
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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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2.75-2.83 | 0.3408 | 129 | 0.301 | 2497 | X-RAY DIFFRACTION | 100 | 2.83-2.92 | 0.3325 | 133 | 0.2747 | 2480 | X-RAY DIFFRACTION | 100 | 2.92-3.03 | 0.3241 | 138 | 0.2665 | 2478 | X-RAY DIFFRACTION | 100 | 3.03-3.15 | 0.2744 | 137 | 0.2708 | 2503 | X-RAY DIFFRACTION | 100 | 3.15-3.29 | 0.2428 | 125 | 0.2392 | 2509 | X-RAY DIFFRACTION | 100 | 3.29-3.46 | 0.257 | 155 | 0.2305 | 2487 | X-RAY DIFFRACTION | 100 | 3.46-3.68 | 0.315 | 140 | 0.2256 | 2519 | X-RAY DIFFRACTION | 100 | 3.68-3.97 | 0.2569 | 122 | 0.2022 | 2546 | X-RAY DIFFRACTION | 100 | 3.97-4.36 | 0.1729 | 155 | 0.1619 | 2519 | X-RAY DIFFRACTION | 100 | 4.36-5 | 0.1738 | 105 | 0.1485 | 2593 | X-RAY DIFFRACTION | 100 | 5-6.29 | 0.2039 | 162 | 0.1847 | 2566 | X-RAY DIFFRACTION | 100 | 6.29-47.44 | 0.1879 | 116 | 0.1824 | 2762 | X-RAY DIFFRACTION | 100 |
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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 | 3.8557 | 2.6269 | -3.769 | 2.9734 | -3.5807 | 5.3606 | -1.8867 | 1.0303 | 0.609 | -0.1867 | 1.312 | 0.0131 | 0.5056 | -0.4096 | 0.6888 | 0.6606 | 0.1492 | -0.0712 | 0.6115 | -0.1169 | 0.5323 | -45.9584 | -16.3887 | -23.2755 | 2 | 1.7243 | -0.9215 | -1.129 | 1.3999 | 0.1761 | 8.2543 | 0.1224 | 0.3569 | 0.532 | 0.4492 | 0.0055 | 0.7041 | 0.4477 | -0.9603 | 0.0738 | 0.394 | -0.0711 | 0.0202 | 0.4788 | -0.023 | 0.7597 | -57.1404 | -12.6226 | -5.0622 | 3 | 8.2669 | 1.2044 | -4.6558 | 7.0744 | -3.7498 | 5.1404 | -0.3474 | 1.0188 | 0.1552 | -0.4953 | 0.3528 | 0.3688 | 0.9966 | -1.5256 | -0.2138 | 0.4505 | -0.1262 | -0.0829 | 0.7412 | -0.1587 | 0.6416 | -61.1145 | -14.6006 | -16.026 | 4 | 7.9919 | 1.1951 | 1.0293 | 4.2092 | -4.418 | 5.8462 | -0.2881 | 1.0897 | 0.866 | -0.7358 | 0.1964 | -0.2187 | -0.3285 | 1.4101 | 0.147 | 0.6262 | -0.0211 | -0.1134 | 0.7899 | -0.1503 | 0.5952 | -52.8017 | -17.4194 | -24.6373 | 5 | 2.4095 | 0.382 | 3.0191 | 3.961 | 0.232 | 4.0691 | 0.2766 | -0.6247 | -0.0749 | 0.5366 | 0.1229 | -0.1996 | 0.344 | 0.0828 | -0.3712 | 0.4149 | -0.0549 | -0.0317 | 0.5619 | 0.0495 | 0.6537 | -56.1458 | -8.572 | 0.7756 | 6 | 8.4196 | -2.2172 | -2.9606 | 3.995 | 0.3482 | 8.3976 | 0.2543 | 1.2728 | 0.0056 | -0.5631 | -0.1751 | 0.0596 | -0.8608 | -0.4151 | 0.0442 | 0.4852 | -0.0066 | -0.0797 | 0.4519 | -0.031 | 0.4699 | -54.9112 | -4.9994 | -15.9428 | 7 | 6.3839 | 2.1529 | -4.5626 | 4.7605 | 0.8869 | 7.4821 | -0.2164 | 0.4736 | 0.6972 | 0.0082 | 0.2564 | 0.4096 | 0.1959 | -0.2037 | 0.0705 | 0.3783 | 0.0399 | -0.0939 | 0.5097 | -0.0917 | 0.5543 | -56.453 | -3.1711 | -8.2311 | 8 | 1.6783 | 0.8546 | 0.3203 | 2.0465 | 0.5035 | 4.7791 | 0.2236 | 0.4087 | 0.1781 | 0.0775 | -0.1113 | -0.8801 | -0.0928 | 0.4498 | 0.0274 | 0.7767 | 0.0302 | 0.0224 | 0.845 | 0.0573 | 0.78 | -37.6652 | -17.6595 | -20.3006 | 9 | 7.091 | 1.5137 | -4.6113 | 2.481 | -2.8762 | 4.6608 | 0.4393 | -0.7947 | -0.3419 | 0.8936 | 0.4716 | -2.3399 | 0.0495 | 2.246 | -0.5687 | 0.4647 | 0.1172 | -0.1628 | 0.9219 | -0.2418 | 0.9248 | -26.7253 | -12.4146 | -0.5925 | 10 | 9.0922 | 2.1061 | -2.1698 | 4.8555 | -1.4546 | 2.87 | -0.4594 | -1.0168 | -1.1121 | -0.5007 | -0.2327 | -0.3944 | 0.677 | -0.1546 | 0.4752 | 0.6144 | 0.0599 | 0.0988 | 0.4808 | 0.0016 | 0.6254 | -45.1884 | -24.2191 | -4.0942 | 11 | 3.4467 | 2.6854 | -2.427 | 5.2607 | -1.4655 | 5.5922 | 0.2517 | -0.4227 | -0.9543 | 0.2564 | -0.5054 | -0.4704 | 0.5505 | 0.5045 | 0.2912 | 0.5969 | 0.1012 | -0.091 | 0.4444 | 0.0301 | 0.6737 | -33.9813 | -27.5721 | -2.1674 | 12 | 7.896 | -0.4617 | -1.0068 | 4.6684 | -0.74 | 4.078 | -0.9814 | -0.4858 | 0.6812 | 0.1816 | 0.3668 | 0.0422 | -0.0695 | -0.0881 | 0.497 | 0.3469 | 0.1144 | -0.0247 | 0.3337 | -0.0884 | 0.593 | -34.0015 | -20.3346 | -0.0831 | 13 | 2.817 | -2.1919 | -1.83 | 3.976 | 0.0986 | 9.8906 | -0.0277 | 0.1057 | -0.7742 | 0.0354 | 0.207 | 0.636 | -0.0969 | -0.9223 | -0.2594 | 0.5142 | -0.0214 | -0.0352 | 0.4673 | -0.0572 | 0.8963 | -54.3767 | -23.517 | -11.5206 | 14 | 6.1212 | 1.4262 | 0.5287 | 5.2468 | -0.0972 | 2.5693 | -0.1233 | 0.3988 | -0.0648 | -0.4593 | 0.0745 | -0.7729 | 0.3139 | 0.3504 | -0.031 | 0.4048 | 0.1173 | 0.034 | 0.4984 | 0.0189 | 0.579 | -34.1279 | -21.5429 | -11.8498 | 15 | 2.9964 | 1.7353 | 1.1445 | 3.6729 | -2.8457 | 6.2438 | -0.2777 | 0.6063 | -0.2317 | -0.9925 | 0.0234 | 0.0317 | 1.0457 | 0.2572 | 0.2474 | 0.5122 | 0.0946 | -0.0079 | 0.474 | -0.0754 | 0.6097 | -41.9213 | -23.2374 | -13.6808 | 16 | 6.0316 | 2.3094 | 1.1845 | 3.2472 | -0.321 | 2.1131 | -0.2728 | 0.2092 | 0.3743 | -0.6723 | 0.7026 | -1.1638 | -0.0854 | -0.5025 | 0.0319 | 0.7374 | -0.017 | 0.136 | 0.6231 | -0.0921 | 0.9476 | -29.6728 | -4.1205 | 0.7909 | 17 | 2.4755 | -2.4161 | 0.2846 | 8.1079 | -0.3065 | 3.6473 | -0.0514 | -0.1575 | 0.1186 | 0.2948 | 0.0631 | 0.1621 | -0.0475 | -0.1438 | -0.0288 | 0.359 | -0.0087 | 0.0272 | 0.4513 | -0.0416 | 0.4329 | -45.9728 | -6.4526 | 6.5939 | 18 | 3.3582 | -2.1043 | 0.9802 | 7.4965 | -1.4895 | 6.3306 | -0.2724 | -0.4214 | 0.7496 | 0.1605 | 0.2983 | -0.6708 | -0.7451 | 0.246 | -0.1566 | 0.4395 | 0.0094 | 0.0232 | 0.5092 | -0.1603 | 0.7608 | -38.145 | -0.5836 | 4.6206 | 19 | 4.5323 | -0.4216 | -2.2248 | 7.9984 | -1.673 | 3.9546 | 0.0571 | -0.8005 | -0.0039 | -0.056 | -0.0437 | -0.5419 | 0.827 | 1.0742 | -0.3825 | 0.4073 | 0.0865 | 0.0242 | 0.605 | -0.117 | 0.5804 | -36.2284 | -8.3513 | 6.417 | 20 | 2.1227 | -0.7415 | -0.7111 | 7.6734 | 0.8277 | 5.5742 | 0.284 | -0.6422 | 0.7305 | -0.367 | -0.2504 | -0.4935 | -0.6274 | 0.3874 | 0.0399 | 0.6716 | -0.0456 | 0.0116 | 0.5984 | 0.0145 | 0.7959 | -51.081 | 3.2324 | -12.3793 | 21 | 1.7209 | 2.0098 | 0.7122 | 3.1598 | 1.7844 | 1.7698 | 9.2995 | 19.9543 | 1.7779 | -9.3711 | -5.1308 | 1.7215 | -5.5328 | -13.8734 | -4.3376 | 0.9278 | 0.4564 | -0.1822 | 1.3648 | 0.058 | 1.3523 | -48.9734 | 7.592 | -16.4761 | 22 | 4.3157 | 1.128 | -2.2759 | 0.8837 | -0.2754 | 9.771 | -0.0135 | -0.7653 | -0.4504 | 0.2781 | -0.2974 | 0.0026 | 0.17 | 0.2908 | 0.0981 | 0.702 | -0.1253 | 0.0029 | 0.7152 | 0.0327 | 0.7078 | -72.742 | -15.9907 | 18.6357 | 23 | 4.739 | 0.2522 | -0.0701 | 4.5816 | -1.5851 | 1.6204 | 0.1133 | -0.0395 | -1.0299 | 0.1464 | 0.7661 | 0.8944 | 1.9191 | -3.1617 | -0.6236 | 0.9002 | -0.2997 | 0.1313 | 0.793 | 0.0482 | 0.7546 | -76.3661 | -19.3008 | 21.18 | 24 | 3.7976 | -0.878 | 2.0521 | 6.0209 | 1.6975 | 5.6407 | 0.0972 | -0.3732 | -0.5755 | -0.5798 | -0.2279 | 0.2837 | -0.5491 | -1.1034 | -0.1462 | 0.6342 | -0.0409 | 0.0883 | 0.7644 | -0.1208 | 0.6126 | -76.4422 | -7.1526 | 1.0672 | 25 | 9.0693 | 1.595 | -1.4701 | 4.1541 | -2.0671 | 3.4736 | 0.4126 | -1.0486 | 0.0973 | 1.1506 | -0.1815 | -0.2318 | -1.3143 | -0.583 | 0.134 | 0.8012 | -0.1251 | 0.09 | 0.8195 | -0.0184 | 0.552 | -77.841 | -7.7492 | 21.2793 | 26 | 5.0661 | 0.3591 | -1.6549 | 6.7092 | -1.3512 | 6.8958 | -0.2745 | 0.1783 | 1.1428 | 0.3931 | 0.5176 | -0.4032 | -0.3214 | -0.5022 | -0.0476 | 0.5502 | -0.0179 | 0.0769 | 0.7553 | 0.0561 | 0.4878 | -76.4713 | -5.2643 | 13.3816 | 27 | 5.2339 | 4.9198 | -0.7198 | 7.6802 | -0.0587 | 6.7921 | 0.6714 | 1.1641 | -0.985 | 0.6432 | -1.3244 | -0.9466 | -1.8041 | -1.8735 | 0.4857 | 1.2125 | -0.279 | 0.224 | 1.7424 | 0.0731 | 0.9502 | -91.7452 | -23.8979 | 25.6052 | 28 | 3.1556 | -0.3688 | 0.2296 | 7.1807 | -1.1798 | 6.4242 | 0.0369 | -0.15 | -0.3895 | -0.8182 | 0.1452 | 0.1909 | 0.3113 | -1.164 | -0.2655 | 0.5511 | -0.171 | 0.0508 | 1.0476 | 0.0246 | 0.5452 | -86.6522 | -11.2201 | -1.4488 | 29 | 0.7401 | 0.4922 | 0.6296 | 2.773 | -0.503 | 2.7126 | -0.051 | -0.1679 | -0.0443 | -0.1092 | 0.3493 | 0.7152 | -0.1686 | -1.6101 | -0.2366 | 0.7424 | -0.111 | 0.0786 | 1.5948 | 0.0861 | 0.9177 | -92.9089 | -7.4522 | 4.0971 | 30 | 6.3913 | -1.4721 | 1.8609 | 4.735 | -0.2921 | 6.2299 | 0.4282 | 1.2303 | 0.8634 | -1.1944 | -0.0917 | 1.9501 | 1.771 | -1.6395 | -0.267 | 1.0208 | -0.5347 | -0.1146 | 1.1891 | 0.2101 | 1.1926 | -92.9617 | -23.9609 | 9.2015 | 31 | 6.2861 | 1.5375 | -1.2474 | 2.3378 | -1.7656 | 2.7084 | -0.084 | 1.0293 | -1.2077 | -0.1854 | 0.3143 | 0.7336 | 2.7809 | -1.6898 | -0.1441 | 1.573 | -0.7723 | -0.2524 | 1.3424 | 0.0459 | 1.1574 | -90.528 | -34.0059 | 7.715 | 32 | 5.8911 | 1.1991 | -1.532 | 1.7935 | -1.4685 | 2.4066 | -0.7275 | 2.1077 | -0.911 | 0.7334 | 1.1697 | -0.216 | -1.5605 | -0.1403 | -0.3789 | 1.1952 | -0.7284 | -0.5292 | 1.893 | 0.3087 | 1.3432 | -104.0764 | -28.0513 | 5.6477 | 33 | 5.287 | -0.9809 | -0.484 | 4.4247 | -0.093 | 1.3751 | 0.3176 | -0.5757 | 0.9786 | 1.0107 | 0.0313 | 0.713 | 1.3722 | -0.7434 | -0.2821 | 1.6334 | -1.1296 | -0.0121 | 0.4716 | 0.1563 | 1.1003 | -85.5551 | -26.3438 | 6.0593 | 34 | 1.1413 | 0.8454 | 1.1153 | 3.9809 | -2.1333 | 8.836 | 0.1063 | -0.9373 | -0.6247 | -0.4213 | -0.3137 | -1.272 | 1.3646 | -0.5398 | 0.2452 | 1.1037 | -0.3318 | -0.033 | 0.8471 | 0.1381 | 0.7978 | -74.3711 | -25.9701 | 16.6749 | 35 | 7.8827 | 2.077 | 2.9551 | 3.998 | -0.0357 | 6.3502 | 0.2479 | -0.1098 | 0.3412 | 0.4525 | -0.6473 | 0.7353 | 0.889 | -2.3002 | -0.1092 | 1.2656 | -0.4699 | 0.1257 | 1.6733 | -0.2374 | 1.0703 | -90.4076 | -23.0735 | 14.5344 | 36 | 3.98 | -0.2541 | 2.0931 | 3.9872 | 1.7922 | 2.0775 | -0.0186 | -0.9926 | -0.4515 | 0.9501 | 0.2751 | 1.0418 | 1.7226 | -2.4632 | -0.1457 | 1.436 | -0.6314 | 0.166 | 1.6752 | 0.3618 | 1.1036 | -96.0037 | -30.4163 | 18.6423 | 37 | 5.8221 | -1.6271 | 1.4077 | 3.4464 | 2.9344 | 6.5668 | 0.8327 | -0.0675 | -0.72 | 0.5879 | -0.8624 | 1.0247 | 1.9033 | -0.6176 | -0.0351 | 1.316 | -0.375 | 0.0518 | 1.3855 | 0.3246 | 0.9169 | -86.5591 | -28.4901 | 19.0294 | 38 | 4.3605 | -0.0266 | -0.0916 | 6.4933 | 0.518 | 9.3448 | -0.3177 | -1.7527 | 0.3794 | -0.4901 | 1.545 | 0.2921 | 1.2657 | 0.3065 | -0.9423 | 0.7915 | -0.2873 | -0.1473 | 2.3507 | 0.1635 | 1.2213 | -102.662 | -12.3213 | 4.8623 | 39 | 1.9999 | 1.9998 | 2.0001 | 2 | 1.9999 | 2 | -7.2755 | -4.8279 | 8.2177 | -7.1803 | 5.3495 | 11.6277 | -25.5134 | 2.5006 | 1.7675 | 2.0543 | 0.8085 | 0.3724 | 2.5733 | 1.4404 | 1.1742 | -108.5893 | -9.2204 | 6.5736 |
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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 -2 through 2 ) | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 3 through 13 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 14 through 32 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 33 through 39 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 40 through 58 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 59 through 88 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 89 through 102 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 103 through 116 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid -2 through 2 ) | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 3 through 13 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 14 through 32 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 33 through 45 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 46 through 58 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 59 through 88 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 89 through 102 )16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resid 103 through 116 )17 | X-RAY DIFFRACTION | 17 | chain 'C' and (resid -2 through 58 ) | 18 | X-RAY DIFFRACTION | 18 | chain 'C' and (resid 59 through 88 )19 | X-RAY DIFFRACTION | 19 | chain 'C' | | | | | | | | | | | | | | | |
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