Software | Name | Classification |
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XDS | data reductionXDS | data scalingPHASER | phasingMOLREP | phasingPHENIX | refinement | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HOMOLOGY MODEL BASED ON 3OUO Resolution: 3.32→34.124 Å / SU ML: 0.47 / σ(F): 2.02 / Phase error: 27.01 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2678 | 2295 | 5 % |
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Rwork | 0.2397 | - | - |
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obs | 0.241 | 45879 | 99.14 % |
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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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Refinement step | Cycle: LAST / Resolution: 3.32→34.124 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 22844 | 0 | 0 | 0 | 22844 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.003 | 23230 | X-RAY DIFFRACTION | f_angle_d0.713 | 31352 | X-RAY DIFFRACTION | f_dihedral_angle_d10.45 | 8707 | X-RAY DIFFRACTION | f_chiral_restr0.029 | 3587 | X-RAY DIFFRACTION | f_plane_restr0.003 | 4019 | | | | | |
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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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3.3201-3.3922 | 0.3634 | 137 | 0.3425 | 2604 | X-RAY DIFFRACTION | 94 | 3.3922-3.471 | 0.3445 | 144 | 0.3111 | 2739 | X-RAY DIFFRACTION | 99 | 3.471-3.5577 | 0.3341 | 143 | 0.289 | 2709 | X-RAY DIFFRACTION | 100 | 3.5577-3.6538 | 0.3304 | 144 | 0.2895 | 2732 | X-RAY DIFFRACTION | 100 | 3.6538-3.7612 | 0.3025 | 145 | 0.2861 | 2768 | X-RAY DIFFRACTION | 100 | 3.7612-3.8824 | 0.309 | 145 | 0.2773 | 2740 | X-RAY DIFFRACTION | 100 | 3.8824-4.021 | 0.3053 | 144 | 0.2515 | 2751 | X-RAY DIFFRACTION | 100 | 4.021-4.1817 | 0.2509 | 145 | 0.2405 | 2748 | X-RAY DIFFRACTION | 100 | 4.1817-4.3717 | 0.2581 | 143 | 0.223 | 2715 | X-RAY DIFFRACTION | 100 | 4.3717-4.6016 | 0.2591 | 144 | 0.2218 | 2728 | X-RAY DIFFRACTION | 100 | 4.6016-4.8892 | 0.2599 | 143 | 0.225 | 2730 | X-RAY DIFFRACTION | 100 | 4.8892-5.2654 | 0.2569 | 144 | 0.2383 | 2738 | X-RAY DIFFRACTION | 100 | 5.2654-5.793 | 0.283 | 146 | 0.2434 | 2758 | X-RAY DIFFRACTION | 100 | 5.793-6.6259 | 0.2384 | 142 | 0.2327 | 2701 | X-RAY DIFFRACTION | 99 | 6.6259-8.3278 | 0.2068 | 142 | 0.198 | 2709 | X-RAY DIFFRACTION | 98 | 8.3278-34.1258 | 0.203 | 144 | 0.1765 | 2714 | 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 | 0.013 | 0.0197 | 0.0135 | -0.0224 | 0.0745 | 0.0029 | -0.1287 | -0.0275 | -0.1544 | 0.1123 | -0.0194 | 0.2883 | 0.2988 | 0.0196 | -0 | 0.4546 | 0.0292 | 0.0265 | 0.4563 | 0.0283 | 0.9579 | 26.4365 | 23.6023 | -19.5642 | 2 | 0.0455 | 0.0898 | -0.075 | 0.1388 | 0.0686 | 0.0617 | -0.1488 | -0.1006 | -0.4348 | 0.1597 | 0.1295 | 0.1042 | -0.4379 | -0.1252 | -0 | 0.2825 | -0.3339 | -0.5891 | -2.2903 | -3.0742 | -3.3287 | 65.0947 | 24.6924 | -17.9613 | 3 | 0.1673 | -0.0614 | -0.1021 | 0.0586 | -0.0381 | 0.1069 | 0.1567 | 0.008 | -0.0359 | 0.1924 | -0.0299 | 0.0498 | -0.0895 | -0.3539 | 0 | 0.354 | 0.0233 | -0.0053 | 0.2609 | 0.0631 | 0.2312 | 52.8999 | 22.2677 | -2.61 | 4 | -0.0073 | -0.0605 | -0.0779 | 0.0519 | 0.0215 | 0.0942 | -0.1662 | 0.0873 | -0.2779 | -0.1049 | -0.1261 | -0.1036 | 0.0421 | 0.0613 | -0 | 0.3584 | -0.049 | -0.0075 | 0.2523 | -0.1182 | 0.2883 | 69.4718 | 19.5068 | -16.321 | 5 | 0.246 | 0.0483 | 0.003 | 0.1639 | -0.0273 | 0.0681 | -0.2786 | -0.0081 | 0.0914 | -0.0215 | 0.0924 | -0.2395 | -0.0468 | -0.1583 | 0 | 0.326 | 0.0279 | -0.0926 | 0.2634 | -0.0451 | 0.2867 | 88.8851 | 53.9759 | -13.5515 | 6 | 0.117 | 0.0787 | -0.0938 | 0.0328 | -0.0741 | 0.0855 | -0.2896 | -0.4027 | -0.0708 | -0.1053 | 0.0676 | -0.0374 | 0.0397 | -0.2067 | -0 | 0.36 | 0.1248 | -0.1532 | 0.3453 | -0.0177 | 0.3037 | 82.6453 | 42.5225 | 1.3599 | 7 | 0.0374 | 0.0279 | -0.0524 | 0.0055 | -0.0232 | 0.013 | 0.0083 | 0.1188 | -0.0693 | 0.0108 | -0.0616 | -0.0719 | -0.2745 | 0.4115 | -0 | 0.4047 | -0.0037 | -0.0926 | 0.3628 | -0.0455 | 0.5008 | 95.5773 | 55.3483 | -11.0228 | 8 | 0.1919 | 0.273 | 0.2863 | 0.067 | 0.0279 | 0.1332 | 0.0809 | -0.2443 | 0.0946 | -0.3629 | 0.1244 | -0.2604 | 0.1649 | -0.2621 | 0 | 0.235 | -0.0325 | 0.0058 | 0.3417 | 0.1173 | 0.3023 | 75.0098 | 87.635 | -8.8576 | 9 | 0.0295 | 0.0087 | 0.0382 | 0.1487 | -0.0501 | 0.046 | 0.3079 | -0.3161 | -0.1617 | -0.417 | 0.2704 | -0.2121 | 0.1741 | -0.2941 | -0 | -0.1472 | -0.2327 | -0.7032 | 0.56 | 0.2048 | -0.0422 | 77.1158 | 75.9339 | 4.9185 | 10 | 0.0076 | -0.0002 | 0.0251 | 0.0516 | -0.1099 | 0.0279 | 0.0302 | 0.016 | 0.0708 | -0.1324 | -0.055 | -0.0102 | -0.5403 | -0.002 | 0 | 0.3352 | -0.0066 | 0.0373 | 0.4135 | -0.0701 | 0.5335 | 75.1238 | 95.158 | -6.861 | 11 | 0.1906 | -0.1993 | 0.0474 | 0.267 | 0.0014 | 0.0434 | 0.0977 | -0.1067 | 0.0036 | -0.0189 | -0.1579 | -0.0277 | 0.237 | 0.1062 | 0 | 0.3533 | 0.0551 | 0.0431 | 0.2591 | 0.0281 | 0.1952 | 36.9836 | 94.6654 | -11.756 | 12 | 0.036 | -0.0588 | 0.0384 | -0.0012 | -0.0526 | -0.0607 | -0.6226 | -0.0803 | -0.4209 | 0.4312 | -0.4978 | -0.3626 | -0.2066 | 0.1782 | 0 | -1.4556 | 0.2259 | -2.3004 | 0.4803 | 0.3662 | -1.1459 | 48.7947 | 93.5296 | 4.1998 | 13 | 0.0901 | -0.1599 | 0.1077 | 0.0874 | -0.0514 | 0.0122 | 0.0752 | 0.0222 | -0.1322 | -0.0235 | -0.2181 | 0.0081 | -0.1743 | -0.0665 | -0 | -0.1537 | -0.4054 | 0.0776 | -0.1172 | -0.1 | 0.6045 | 32.718 | 99.755 | -9.2161 | 14 | 0.1312 | 0.0069 | -0.0495 | 0.0898 | 0.061 | 0.0531 | -0.3829 | -0.6672 | -0.1739 | -0.2717 | -0.2529 | 0.4626 | 0.1598 | 0.0971 | 0 | 0.611 | 0.0383 | -0.2903 | -0.4139 | -0.1384 | 1.8028 | 13.9529 | 65.0283 | -11.2448 | 15 | 0.0133 | 0.0078 | 0.0189 | 0.0059 | -0.0342 | 0.0223 | -0.0794 | 0.0201 | 0.1453 | 0.1471 | -0.1312 | -0.1481 | -0.1353 | 0.2584 | -0 | 0.8058 | -0.0173 | 0.0106 | 0.6057 | -0.0462 | 0.9133 | 26.0182 | 71.667 | 1.0485 | 16 | 0.0036 | -0.0119 | 0.0172 | -0.0202 | -0.0084 | 0.0005 | -0.1439 | -0.1419 | 0.0602 | 0.0201 | -0.2614 | 0.1442 | 0.0626 | 0.0127 | -0 | 1.0716 | -0.0378 | -0.0844 | 0.8548 | -0.0011 | 0.9677 | 18.6445 | 73.1383 | 11.5066 | 17 | 0.0766 | 0.0424 | -0.0049 | 0.0435 | -0.0184 | -0.0226 | 0.2035 | 0.163 | 0.2168 | -0.0153 | 0.2465 | 0.3578 | 0.3752 | -0.2095 | 0 | 0.8125 | 0.2335 | -0.0872 | 0.8514 | -0.0132 | 0.9969 | 11.96 | 52.9176 | -15.7588 | 18 | 0.0362 | 0.0406 | -0.003 | 0.0414 | 0.0065 | 0.066 | -0.1262 | 0.2747 | 0.3268 | -0.1774 | -0.1607 | -0.0186 | -0.1757 | 0.1704 | 0 | 0.4589 | 0.0235 | -0.0765 | 0.4427 | 0.0109 | 0.4878 | 29.2584 | 31.4194 | -22.2719 | 19 | 0.0089 | -0.0408 | 0.0065 | -0.0017 | 0.0875 | 0.0837 | -0.0116 | -0.7217 | 0.2212 | 0.4384 | 0.036 | 0.3082 | -0.019 | -0.0228 | -0 | 0.871 | 0.0004 | 0.0565 | 0.8972 | -0.039 | 0.762 | 22.6694 | 34.1941 | -1.8948 | 20 | 0.0275 | 0.06 | 0.0491 | 0.0189 | 0.1196 | 0.0875 | 0.204 | -0.0215 | -0.017 | 0.4269 | -0.0177 | 0.1995 | 0.6097 | -0.1016 | 0 | 0.3895 | 0.0221 | 0.0828 | 0.3807 | -0.0321 | 0.529 | 18.7006 | 39.1279 | -57.2118 | 21 | 0.1318 | 0.0597 | 0.0409 | 0.1022 | 0.0557 | 0.1019 | -0.2742 | -0.764 | -1.0943 | 0.1102 | 0.365 | 0.3407 | -0.1313 | -0.1619 | 0 | 0.2717 | -0.1584 | -0.3621 | -0.6099 | -1.3219 | -1.1179 | 54.8591 | 28.1211 | -60.3921 | 22 | 0.0792 | -0.0703 | -0.0899 | 0.0876 | 0.0545 | 0.0201 | -0.0311 | -0.3634 | 0.1852 | -0.0771 | 0.0275 | 0.2876 | -0.0901 | -0.0834 | -0 | 0.346 | -0.0575 | -0.0024 | 0.376 | -0.1019 | 0.3968 | 45.1264 | 31.6417 | -45.2791 | 23 | 0.0151 | -0.0094 | -0.0454 | 0.0069 | -0.0051 | 0.0725 | -0.0338 | -0.0158 | -0.0529 | -0.0839 | -0.0007 | -0.0642 | 0.3112 | -0.0162 | 0 | 0.3598 | 0.0063 | -0.0651 | 0.3238 | -0.0404 | 0.3571 | 56.8653 | 21.4756 | -60.5022 | 24 | 0.182 | 0.137 | 0.0307 | 0.1045 | -0.12 | 0.0792 | 0.1928 | -0.3905 | 0.317 | -0.2927 | -0.2485 | -0.3675 | -0.0133 | -0.177 | -0 | 0.3305 | -0.0277 | 0.0827 | 0.5494 | -0.106 | 0.4679 | 88.3689 | 47.4365 | -56.2049 | 25 | 0.1215 | 0.0456 | -0.0458 | 0.0359 | 0.0089 | 0.052 | -0.0905 | -0.8488 | 0.1144 | 0.135 | -0.4704 | 0.1367 | -0.0132 | -0.1528 | -0 | 0.3258 | 0.0433 | 0.1405 | 0.7057 | -0.0837 | -0.0657 | 75.7519 | 40.3793 | -42.6614 | 26 | 0.0333 | 0.0005 | -0.0319 | 0.0033 | 0.0366 | 0.039 | -0.0447 | -0.105 | -0.1135 | -0.0324 | -0.009 | -0.1055 | -0.1057 | 0.2375 | 0 | 0.4202 | 0.0041 | -0.0488 | 0.6428 | 0.1009 | 0.832 | 94.0944 | 46.9008 | -52.4064 | 27 | 0.3828 | 0.0474 | -0.2637 | 0.2483 | 0.0354 | 0.157 | 0.0271 | -0.0007 | 0.0952 | 0.0158 | 0.0122 | 0.0133 | 0.2125 | 0.1023 | 0 | 0.4034 | 0.1069 | 0.0858 | 0.4853 | 0.0651 | 0.4321 | 86.9041 | 79.8516 | -48.5387 | 28 | 0.0193 | 0.0177 | 0.0281 | -0.0232 | -0.0573 | 0.2545 | -0.0595 | 0.3252 | 0.0339 | -0.2882 | 0.1982 | -0.1963 | -0.3257 | 0.1605 | -0 | 0.4624 | 0.0348 | 0.1196 | 0.495 | -0.0331 | 0.6444 | 78.3671 | 98.0618 | -56.5699 | 29 | 0.0969 | 0.0251 | 0.0431 | 0.1446 | 0.0217 | 0.0633 | -0.0795 | 0.0864 | 0.0617 | 0.0133 | -0.2173 | -0.2199 | 0.2473 | -0.1998 | -0 | 0.3376 | 0.0739 | -0.0109 | 0.352 | 0.0493 | 0.2689 | 50.0408 | 100.439 | -51.4754 | 30 | 0.1058 | -0.1567 | 0.0424 | 0.0755 | -0.0782 | 0.1074 | -0.0624 | -0.1065 | -0.1463 | 0.121 | 0.0667 | -0.2017 | 0.1462 | 0.0986 | 0 | 0.4101 | 0.0107 | -0.0719 | 0.2821 | 0.037 | 0.3395 | 62.0718 | 93.7356 | -38.5078 | 31 | 0.0257 | -0.053 | -0.0112 | 0.0415 | 0.0233 | 0.0386 | -0.1676 | 0.1245 | -0.0039 | 0.1743 | -0.0832 | 0.0872 | -0.4042 | -0.0035 | -0 | 0.486 | 0.0207 | 0.0409 | 0.3776 | -0.0535 | 0.5954 | 48.8293 | 107.5874 | -49.0334 | 32 | 0.0633 | -0.0035 | 0.0209 | 0.1226 | 0.0118 | 0.0031 | 0.0319 | 0.3006 | 0.1625 | -0.1833 | -0.231 | 0.3663 | 0.016 | 0.1667 | -0 | 0.3213 | 0.2039 | -0.2014 | 0.2046 | -0.07 | 0.4799 | 19.7996 | 83.3325 | -61.2151 | 33 | 0.0365 | 0.0177 | -0.0011 | 0.0131 | -0.0219 | 0.0183 | 0.2125 | -0.3869 | 0.0611 | 0.5517 | 0.1518 | -0.2101 | -0.0459 | 0.074 | -0 | 0.9953 | 0.0833 | -0.12 | 0.3559 | -0.222 | 0.4379 | 28.3054 | 80.9471 | -40.9482 | 34 | 0.0135 | 0.0004 | 0.0411 | 0.0174 | 0.0177 | 0.0293 | -0.0121 | -0.1726 | 0.36 | 0.2426 | -0.34 | -0.1649 | 0.0139 | -0.0062 | -0 | 1.0066 | -0.1215 | 0.1465 | 0.4026 | -0.2896 | 0.5785 | 24.2103 | 91.8806 | -37.809 | 35 | 0.0642 | -0.0263 | 0.0404 | 0.0017 | -0.0011 | 0.0389 | -0.0342 | 0.2718 | 0.0594 | 0.0361 | -0.2297 | 0.055 | -0.0247 | -0.0588 | 0 | 0.4519 | 0.1773 | 0.2372 | 0.2144 | -0.1987 | 1.0614 | 13.1877 | 82.5377 | -55.22 | 36 | 0.03 | 0.0167 | 0.0103 | 0.1077 | 0.0257 | 0.0769 | -0.0383 | 0.4144 | 0.0906 | 0.3733 | -0.0382 | 0.1322 | -0.188 | 0.0368 | -0 | 0.2901 | 0.0689 | -0.0064 | 0.3785 | -0.0793 | 0.2711 | 20.6292 | 44.94 | -63.5403 | 37 | 0.0071 | 0.0937 | 0.0215 | 0.0731 | 0.1792 | 0.0998 | 0.0322 | 0.1799 | 0.5173 | 1.1454 | -0.2049 | 0.1157 | 0.5443 | 0.1695 | -0 | 0.8182 | 0.175 | 0.1899 | -0.3701 | -1.196 | -0.9616 | 23.3744 | 53.4961 | -42.8885 |
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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 5 THROUGH 36 )2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESID 37 THROUGH 147 )3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESID 148 THROUGH 250 )4 | X-RAY DIFFRACTION | 4 | CHAIN B AND (RESID 4 THROUGH 36 )5 | X-RAY DIFFRACTION | 5 | CHAIN B AND (RESID 37 THROUGH 147 )6 | X-RAY DIFFRACTION | 6 | CHAIN B AND (RESID 148 THROUGH 251 )7 | X-RAY DIFFRACTION | 7 | CHAIN C AND (RESID 4 THROUGH 36 )8 | X-RAY DIFFRACTION | 8 | CHAIN C AND (RESID 37 THROUGH 163 )9 | X-RAY DIFFRACTION | 9 | CHAIN C AND (RESID 164 THROUGH 250 )10 | X-RAY DIFFRACTION | 10 | CHAIN D AND (RESID 4 THROUGH 36 )11 | X-RAY DIFFRACTION | 11 | CHAIN D AND (RESID 37 THROUGH 147 )12 | X-RAY DIFFRACTION | 12 | CHAIN D AND (RESID 148 THROUGH 252 )13 | X-RAY DIFFRACTION | 13 | CHAIN E AND (RESID 4 THROUGH 36 )14 | X-RAY DIFFRACTION | 14 | CHAIN E AND (RESID 37 THROUGH 147 )15 | X-RAY DIFFRACTION | 15 | CHAIN E AND (RESID 148 THROUGH 216 )16 | X-RAY DIFFRACTION | 16 | CHAIN E | | | | | | | | | | | | | | | |
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