Software | Name | Version | Classification |
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SCALA | 3.3.20data scalingPHENIX | | refinementPDB_EXTRACT | 3.15 | data extractionSHELX | | phasing | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→47.756 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.84 / Phase error: 22.51 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2129 | 4952 | 4.69 % |
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Rwork | 0.1733 | 100549 | - |
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obs | 0.1753 | 54446 | 92.45 % |
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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 max: 126.8 Å2 / Biso mean: 27.8379 Å2 / Biso min: 8.55 Å2 |
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Refinement step | Cycle: final / Resolution: 1.8→47.756 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4590 | 0 | 48 | 306 | 4944 |
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Biso mean | - | - | 32.15 | 30.53 | - |
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Num. residues | - | - | - | - | 595 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.011 | 4810 | X-RAY DIFFRACTION | f_angle_d1.225 | 6532 | X-RAY DIFFRACTION | f_chiral_restr0.065 | 753 | X-RAY DIFFRACTION | f_plane_restr0.007 | 864 | X-RAY DIFFRACTION | f_dihedral_angle_d11.795 | 1807 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Number | Refine-ID | Rms | Type |
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1 | 1 | A2588 | X-RAY DIFFRACTION | 8.561 | TORSIONAL1 | 2 | B2588 | X-RAY DIFFRACTION | 8.561 | TORSIONAL1 | 3 | C2588 | X-RAY DIFFRACTION | 8.561 | TORSIONAL1 | 4 | D2588 | X-RAY DIFFRACTION | 8.561 | TORSIONAL | | | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8-1.8205 | 0.2816 | 88 | 0.2144 | 1984 | 2072 | 56 | 1.8205-1.8419 | 0.2789 | 136 | 0.2098 | 2432 | 2568 | 66 | 1.8419-1.8644 | 0.2242 | 120 | 0.2049 | 2649 | 2769 | 74 | 1.8644-1.888 | 0.257 | 145 | 0.2018 | 2802 | 2947 | 77 | 1.888-1.9128 | 0.2208 | 142 | 0.2041 | 3012 | 3154 | 83 | 1.9128-1.939 | 0.2119 | 150 | 0.2013 | 3135 | 3285 | 85 | 1.939-1.9667 | 0.229 | 163 | 0.1992 | 3100 | 3263 | 88 | 1.9667-1.9961 | 0.2155 | 149 | 0.2011 | 3335 | 3484 | 90 | 1.9961-2.0273 | 0.2333 | 171 | 0.196 | 3369 | 3540 | 94 | 2.0273-2.0605 | 0.2256 | 185 | 0.1942 | 3492 | 3677 | 95 | 2.0605-2.096 | 0.255 | 169 | 0.1858 | 3471 | 3640 | 97 | 2.096-2.1341 | 0.1978 | 176 | 0.1707 | 3496 | 3672 | 97 | 2.1341-2.1752 | 0.2228 | 158 | 0.1678 | 3583 | 3741 | 98 | 2.1752-2.2196 | 0.1926 | 188 | 0.18 | 3539 | 3727 | 98 | 2.2196-2.2678 | 0.2789 | 179 | 0.186 | 3534 | 3713 | 97 | 2.2678-2.3206 | 0.2128 | 176 | 0.1714 | 3577 | 3753 | 99 | 2.3206-2.3786 | 0.2337 | 156 | 0.174 | 3564 | 3720 | 98 | 2.3786-2.4429 | 0.2149 | 175 | 0.1664 | 3533 | 3708 | 98 | 2.4429-2.5148 | 0.2563 | 176 | 0.1799 | 3578 | 3754 | 98 | 2.5148-2.596 | 0.2072 | 168 | 0.1805 | 3570 | 3738 | 99 | 2.596-2.6888 | 0.2075 | 190 | 0.1845 | 3605 | 3795 | 99 | 2.6888-2.7964 | 0.2283 | 176 | 0.176 | 3549 | 3725 | 99 | 2.7964-2.9237 | 0.219 | 182 | 0.1847 | 3552 | 3734 | 99 | 2.9237-3.0778 | 0.2282 | 179 | 0.1873 | 3594 | 3773 | 98 | 3.0778-3.2706 | 0.2111 | 169 | 0.1802 | 3569 | 3738 | 99 | 3.2706-3.523 | 0.2315 | 173 | 0.1647 | 3596 | 3769 | 99 | 3.523-3.8774 | 0.1818 | 181 | 0.1532 | 3608 | 3789 | 99 | 3.8774-4.4381 | 0.1806 | 176 | 0.139 | 3577 | 3753 | 99 | 4.4381-5.5902 | 0.1717 | 188 | 0.1554 | 3587 | 3775 | 99 | 5.5902-47.773 | 0.2225 | 168 | 0.1731 | 3557 | 3725 | 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 | 0.6274 | -0.1073 | 0.1986 | 2.2745 | -0.2647 | 0.6321 | 0.4952 | -0.5709 | 0.1181 | -0.0323 | -0.3953 | -0.6365 | -0.0613 | 0.0368 | 0.1519 | 0.0957 | -0.0789 | -0.1772 | 0.2632 | -0.0055 | 0.008 | 76.0882 | 36.7202 | 39.4162 | 2 | 0.5584 | 0.1672 | 0.0133 | 0.1862 | -0.2892 | 0.485 | 0.072 | -0.1279 | 0.0504 | 0.033 | -0.0657 | 0.018 | -0.0188 | 0.0111 | -0.0765 | 0.1417 | 0.0014 | 0.025 | 0.0903 | 0.0212 | 0.1628 | 71.8814 | 42.2614 | 30.5456 | 3 | 1.4943 | 0.3762 | 0.0639 | 0.6425 | 0.442 | 0.2434 | 0.0584 | -0.0249 | 0.029 | 0.109 | -0.0841 | -0.0084 | 0.0208 | -0.0692 | 0.0469 | 0.1434 | 0.0049 | 0.036 | 0.1171 | 0.0117 | 0.1635 | 68.6163 | 42.7078 | 28.3449 | 4 | 0.3466 | -0.2713 | -0.1113 | 0.2319 | 0.1257 | 0.0983 | -0.088 | 0.2545 | -0.3557 | -0.0926 | -0.0181 | 0.0186 | 0.0601 | -0.0802 | -0.1569 | 0.1583 | -0.0315 | 0.0294 | 0.1818 | -0.0533 | 0.1522 | 66.0608 | 33.8567 | 20.7867 | 5 | 0.1098 | -0.2761 | 0.0937 | 0.8328 | 0.4585 | 1.8711 | -0.1795 | 0.2494 | -0.5278 | -0.117 | -0.1494 | -0.0592 | 0.0105 | -0.1583 | -0.6848 | 0.2274 | 0.0142 | 0.1332 | 0.1616 | -0.0471 | 0.4106 | 71.4252 | 27.0929 | 27.5864 | 6 | 1.4859 | -0.0548 | -0.2917 | 0.1742 | -0.1654 | 0.6296 | -0.2086 | -0.4869 | -0.4861 | 0.0455 | -0.0457 | -0.0854 | 0.3302 | 0.2842 | -0.0886 | 0.2974 | 0.0871 | 0.0826 | 0.1634 | 0.1176 | 0.3116 | 75.5937 | 26.775 | 38.9422 | 7 | 3.1694 | -0.578 | -0.0081 | 0.4281 | -0.2137 | 0.4115 | 0.0412 | 0.6959 | -1.1307 | -0.0626 | -0.1579 | 0.4531 | 0.2728 | -0.0432 | -0.018 | 0.238 | 0.0412 | 0.0879 | 0.0732 | 0.0586 | 0.3805 | 77.3984 | 27.9886 | 23.3621 | 8 | 0.0502 | -0.05 | 0.0282 | 0.0908 | -0.0914 | 0.1709 | -0.1564 | -0.0658 | 0.2097 | -0.0312 | -0.0612 | -0.0337 | -0.2895 | 0.271 | -0.0067 | 0.2371 | 0.0471 | 0.0574 | 0.2364 | 0.0141 | 0.2591 | 85.6343 | 35.9197 | 27.5161 | 9 | 0.1528 | 0.0827 | -0.0528 | 0.3374 | 0.1325 | 0.1806 | 0.1863 | 0.2186 | 0.2853 | 0.0283 | -0.0148 | -0.0652 | -0.4705 | -0.2822 | -0.0936 | 0.1714 | 0.0376 | 0.0473 | 0.1563 | 0.0255 | 0.258 | 48.1605 | 42.5947 | 38.0919 | 10 | 0.5955 | -0.504 | 0.1848 | 0.7872 | 0.3245 | 0.446 | 0.081 | -0.108 | 0.2943 | -0.0012 | -0.1078 | -0.1208 | -0.0389 | 0.101 | -0.2218 | 0.1384 | -0.0308 | 0.0186 | 0.151 | -0.0334 | 0.1719 | 52.2041 | 36.9583 | 49.0124 | 11 | 6.4925 | 2.2581 | 0.4487 | 1.7325 | -0.5992 | 0.6606 | 0.2739 | 0.5129 | 0.5742 | -0.196 | -0.1901 | -0.2733 | -0.312 | -0.15 | 0.0275 | 0.2839 | -0.0605 | 0.0396 | 0.1711 | -0.1317 | 0.2672 | 48.3688 | 45.7509 | 52.8079 | 12 | 0.3523 | -0.4399 | 0.1024 | 0.8311 | -0.2698 | 0.9627 | 0.3281 | -0.4142 | 0.283 | 0.1309 | -0.2644 | -0.4171 | 0.1098 | 0.2869 | -0.041 | 0.1467 | -0.0485 | -0.023 | 0.2097 | -0.0023 | 0.1995 | 60.2731 | 31.9036 | 50.39 | 13 | 0.4853 | 0.3458 | -0.1856 | 0.1477 | -0.1192 | 0.3715 | 0.0016 | -0.1164 | -0.1191 | -0.0451 | -0.003 | -0.1566 | 0.0826 | 0.1897 | -0.0098 | 0.1567 | -0.0044 | -0.0085 | 0.1465 | -0.008 | 0.149 | 55.0477 | 24.6342 | 46.709 | 14 | 1.2587 | -0.0223 | 0.8604 | 0.8323 | -0.0295 | 0.8326 | -0.0213 | -0.1638 | -0.194 | 0.1597 | 0.0742 | -0.0048 | 0.3084 | -0.1396 | 0.045 | 0.1488 | -0.0241 | 0.0218 | 0.1303 | -0.0055 | 0.1687 | 47.367 | 27.0879 | 43.7024 | 15 | 0.3865 | 0.1569 | 0.4695 | 0.1985 | 0.3402 | 0.7267 | -0.1212 | 0.7722 | 0.1837 | -0.0213 | 0.3286 | 0.0923 | -0.1933 | -0.1221 | 0.3366 | 0.2339 | -0.0866 | -0.0132 | 0.2456 | 0.1011 | 0.1759 | 44.7234 | 36.7289 | 32.5791 | 16 | 0.1093 | 0.0588 | -0.0667 | 0.136 | 0.1407 | 0.1823 | 0.0152 | 0.2041 | -0.0444 | 0.0413 | 0.0127 | 0.2553 | 0.0204 | 0.0167 | -0.0034 | 0.1597 | -0.014 | -0.0144 | 0.1418 | 0.0044 | 0.1685 | 40.1169 | 26.3842 | 43.0347 | 17 | 0.0189 | 0.0142 | -0.0204 | 0.0108 | -0.017 | -0.0002 | 0.1329 | -0.0314 | 0.374 | 0.3289 | -0.3169 | 0.5022 | -0.0759 | -0.3911 | -0.0005 | 0.1914 | -0.0128 | 0.0264 | 0.175 | -0.041 | 0.1796 | 38.1028 | 30.2599 | 52.9556 | 18 | 0.0836 | 0.2562 | 0.1689 | 0.6561 | 0.4627 | 0.4767 | 0.3737 | 0.724 | -0.3466 | -0.3726 | -0.6666 | 0.2412 | -0.0792 | -0.2053 | -0.0448 | 0.2262 | 0.1346 | -0.036 | 0.4476 | -0.0031 | 0.2194 | 33.9071 | 34.7115 | 41.3271 | 19 | 0.4449 | 0.067 | 0.0822 | 1.2839 | 0.0695 | 0.4879 | 0.2075 | 0.1156 | -0.2427 | -0.2536 | -0.3201 | 0.1613 | -0.2855 | -0.4624 | -0.7976 | 0.2291 | 0.0259 | -0.0707 | 0.2502 | -0.0166 | 0.1021 | 9.9855 | 52.8573 | 47.1505 | 20 | 0.4471 | -0.0462 | 0.3326 | 0.1809 | -0.2866 | 0.4752 | -0.0925 | -0.0409 | -0.013 | 0.0646 | 0.02 | -0.0004 | -0.0148 | -0.0809 | -0.1557 | 0.1031 | -0.001 | -0.0189 | 0.1147 | -0.0116 | 0.0839 | 17.0212 | 46.4303 | 54.1241 | 21 | 0.6398 | 0.3787 | -0.3557 | 0.6597 | -0.1135 | 0.9323 | -0.0537 | -0.1508 | -0.0718 | -0.0742 | 0.0175 | 0.0057 | 0.0016 | -0.1332 | -0.0752 | 0.1202 | 0.0069 | -0.0074 | 0.1504 | 0.0018 | 0.1046 | 17.9066 | 45.8318 | 57.9231 | 22 | 1.0831 | 0.4088 | -1.2229 | 0.7736 | -0.7897 | 1.6294 | 0.0997 | -0.2454 | -0.0205 | 0.464 | 0.1021 | -0.2391 | -0.9765 | 0.6418 | 0.1848 | 0.2619 | -0.0725 | -0.0922 | 0.3181 | -0.0423 | 0.144 | 23.5004 | 56.317 | 67.4625 | 23 | 0.2719 | -0.1112 | 0.261 | 0.6804 | 0.106 | 0.406 | 0.1203 | -0.2672 | -0.0774 | -0.1794 | 0.1087 | -0.1988 | -0.1308 | 0.1806 | 0.2558 | 0.0421 | -0.018 | -0.036 | 0.1777 | -0.0162 | 0.1228 | 25.115 | 51.3457 | 57.0853 | 24 | 0.9064 | 0.8611 | 0.0323 | 1.1288 | -0.01 | 0.8568 | 0.1175 | -0.0163 | 0.4566 | -0.0393 | -0.1203 | -0.312 | -0.2339 | 0.173 | 0.404 | 0.2518 | -0.0534 | 0.0309 | 0.2007 | 0.001 | 0.2899 | 19.6446 | 61.6363 | 56.0808 | 25 | 0.0288 | -0.0282 | 0.0043 | 0.0752 | -0.0036 | 0.1188 | 0.131 | 0.4625 | 0.4794 | -0.2708 | 0.0749 | -0.1045 | -0.3084 | -0.0505 | 0.0095 | 0.2905 | 0.0422 | 0.0196 | 0.1905 | 0.0607 | 0.2336 | 10.638 | 62.2341 | 48.1198 | 26 | 0.8916 | -0.3504 | 0.5599 | 0.6777 | 0.4405 | 1.3414 | 0.2085 | 0.0598 | 0.6519 | -0.2052 | 0.0432 | -0.3203 | -0.7586 | 0.268 | 0.2688 | 0.2033 | -0.0572 | -0.0234 | 0.2 | 0.0176 | 0.1904 | 25.958 | 60.8144 | 51.8212 | 27 | 0.5012 | 0.5376 | -0.0949 | 1.1026 | 0.5577 | 2.4183 | 0.2724 | 0.136 | -0.007 | -0.6149 | 0.2588 | -0.4524 | -0.8976 | 0.3741 | 0.9518 | 0.404 | -0.0086 | 0.0389 | 0.1358 | 0.0378 | 0.1629 | 26.7443 | 54.9321 | 44.1975 | 28 | 1.6666 | 1.5018 | -0.3867 | 1.5352 | -0.3062 | 0.7483 | -0.1824 | -0.0703 | -0.7231 | -0.2369 | -0.2694 | -0.7538 | 0.6131 | 0.599 | -0.4524 | 0.3816 | -0.0056 | 0.1209 | 0.3277 | 0.0292 | 0.2088 | 20.6475 | 49.6711 | 36.9883 | 29 | 0.8049 | -0.3369 | -0.2647 | 0.413 | 0.1716 | 0.2532 | -0.5121 | -0.4032 | -0.8232 | 0.2558 | 0.1917 | 0.2314 | 0.3194 | 0.1633 | -0.0313 | 0.2019 | 0.0273 | 0.0294 | 0.1705 | 0.0371 | 0.1944 | 1.5244 | 45.7859 | 73.6527 | 30 | 0.4582 | 0.1697 | -0.171 | 0.4667 | -0.2467 | 0.6845 | -0.1395 | 0.1724 | -0.2103 | -0.1143 | 0.0181 | 0.042 | 0.2498 | -0.076 | -0.0511 | 0.1171 | -0.0415 | -0.0009 | 0.171 | -0.0301 | 0.1661 | -7.2656 | 51.2235 | 65.9555 | 31 | 2.4357 | 1.5041 | -1.5683 | 1.1582 | -0.6999 | 1.5538 | -0.1454 | 0.1183 | -0.4669 | -0.1489 | -0.1846 | -0.3882 | 0.1804 | -0.0756 | -0.585 | 0.1868 | -0.0493 | -0.0189 | 0.2194 | -0.0681 | 0.1492 | -8.5324 | 50.3254 | 62.3634 | 32 | 0.2423 | 0.0378 | -0.0506 | 0.6297 | 0.2409 | 0.3291 | -0.0222 | 0.1191 | -0.0846 | -0.3238 | 0.0224 | -0.1494 | -0.1142 | -0.1032 | -0.0158 | 0.1517 | -0.0214 | -0.0274 | 0.1778 | 0.0017 | 0.1379 | -4.2634 | 63.4242 | 63.9109 | 33 | 0.1854 | -0.074 | 0.134 | 0.8509 | -0.4173 | 1.7595 | -0.019 | -0.1119 | 0.1522 | 0.0767 | 0.1326 | 0.0701 | -0.0176 | -0.1321 | 0.153 | 0.1362 | 0.0127 | -0.0028 | 0.1382 | -0.02 | 0.1805 | -3.9675 | 61.2997 | 72.3709 | 34 | 0.5069 | 0.3211 | 0.0026 | 0.3828 | 0.0602 | 0.1633 | -0.0876 | -0.2725 | 0.0347 | 0.2477 | 0.1902 | -0.0482 | 0.0434 | 0.2357 | 0.1783 | 0.1619 | 0.0629 | -0.0244 | 0.1813 | -0.015 | 0.1332 | -1.3143 | 57.9319 | 78.8705 | 35 | 0.3574 | 0.5363 | 0.1693 | 0.6682 | 0.2025 | 0.2567 | -0.0767 | -0.159 | -0.1272 | 0.2173 | -0.0812 | 0.1717 | 0.0982 | 0.0222 | -0 | 0.2511 | 0.0172 | 0.0597 | 0.2074 | 0.0382 | 0.1717 | -9.2009 | 54.7005 | 80.5473 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 40 through 58 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 59 through 84 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 85 through 119 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 120 through 139 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 140 through 151 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 152 through 160 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 161 through 171 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 172 through 194 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 38 through 58 )B0 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 59 through 84 )B0 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 85 through 93 )B0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 94 through 105 )B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 106 through 130 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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