Software | Name | Version | Classification |
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PHENIX | (1.13_2998: ???)refinementAimless | 0.7.4data scalingXDS | BUILT 20230630data reductionPHASER | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.089→41.734 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2397 | 1541 | 4.89 % |
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Rwork | 0.2138 | - | - |
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obs | 0.215 | 31510 | 99.86 % |
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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: 3.089→41.734 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10578 | 0 | 150 | 0 | 10728 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.003 | 11010 | X-RAY DIFFRACTION | f_angle_d0.626 | 14998 | X-RAY DIFFRACTION | f_dihedral_angle_d13.145 | 6202 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 1702 | X-RAY DIFFRACTION | f_plane_restr0.003 | 1812 | | | | | |
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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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3.089-3.1885 | 0.286 | 157 | 0.2878 | 2705 | X-RAY DIFFRACTION | 100 | 3.1885-3.3024 | 0.3362 | 141 | 0.2809 | 2727 | X-RAY DIFFRACTION | 100 | 3.3024-3.4346 | 0.3118 | 145 | 0.2712 | 2694 | X-RAY DIFFRACTION | 100 | 3.4346-3.5908 | 0.2991 | 133 | 0.2225 | 2723 | X-RAY DIFFRACTION | 100 | 3.5908-3.78 | 0.2469 | 140 | 0.215 | 2713 | X-RAY DIFFRACTION | 100 | 3.78-4.0167 | 0.2266 | 119 | 0.2185 | 2750 | X-RAY DIFFRACTION | 100 | 4.0167-4.3265 | 0.2272 | 119 | 0.1993 | 2738 | X-RAY DIFFRACTION | 100 | 4.3265-4.7614 | 0.2293 | 158 | 0.1807 | 2719 | X-RAY DIFFRACTION | 100 | 4.7614-5.4491 | 0.2019 | 138 | 0.201 | 2706 | X-RAY DIFFRACTION | 100 | 5.4491-6.8603 | 0.24 | 159 | 0.2449 | 2734 | X-RAY DIFFRACTION | 100 | 6.8603-41.734 | 0.2187 | 132 | 0.1924 | 2760 | X-RAY DIFFRACTION | 99 |
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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 | 6.1678 | -1.5098 | -3.9883 | 3.7384 | -0.0152 | 7.8188 | 0.1044 | -0.3694 | -0.1162 | -0.1184 | -0.2137 | -0.2427 | 0.6445 | 1.57 | 0.2779 | 0.2762 | 0.1052 | -0.1288 | 0.6346 | 0.0183 | 0.7824 | 48.8298 | 29.2263 | 40.234 | 2 | 3.6156 | 0.2622 | -1.2498 | 2.7112 | -0.9886 | 5.8737 | -0.0797 | 1.1162 | 0.4141 | -0.7272 | -0.0429 | -0.285 | -0.4382 | -0.2172 | 0.147 | 0.8499 | 0.0911 | -0.0611 | 1.061 | 0.163 | 0.5399 | 29.6083 | 40.3333 | 8.3731 | 3 | 1.446 | -0.069 | 0.2002 | 2.3495 | -2.0546 | 5.1622 | -0.0206 | 0.3694 | 0.3497 | -0.2537 | -0.2209 | -0.1511 | -0.2307 | 0.1411 | 0.2436 | 0.555 | 0.1221 | -0.0786 | 0.6775 | 0.0255 | 0.5791 | 31.5458 | 41.0418 | 22.4953 | 4 | 7.4222 | -2.7352 | -6.4955 | 2.2943 | 1.8332 | 5.8923 | 0.3227 | 1.6941 | -0.1551 | -0.6227 | -0.5394 | -0.1448 | -0.1251 | -1.0284 | 0.1995 | 0.9012 | 0.0725 | -0.0745 | 1.154 | -0.0096 | 0.4157 | 34.3361 | 25.7511 | 5.9906 | 5 | 5.625 | -0.7061 | 5.6182 | 7.2714 | 0.3618 | 9.8178 | 0.5443 | 0.4692 | -0.064 | 0.8656 | -0.3966 | 1.0922 | 2.4495 | 0.3951 | -0.2455 | 0.6315 | 0.1063 | 0.1729 | 0.5355 | -0.04 | 0.5921 | 20.828 | 10.3658 | 45.9468 | 6 | 4.11 | -1.3307 | -0.2851 | 5.7224 | 0.3106 | 6.256 | -0.1885 | -0.5951 | 0.51 | 0.3981 | -0.0521 | -0.1801 | -0.3507 | 0.5896 | 0.2546 | 0.5279 | 0.0342 | -0.1817 | 0.6913 | -0.0945 | 0.6322 | 36.3803 | 45.6249 | 53.0696 | 7 | 2.9688 | 2.3745 | 0.1584 | 2.491 | 0.7989 | 1.5002 | 0.0758 | -0.4388 | 0.3975 | 0.3171 | -0.2474 | 0.6717 | -0.0178 | -0.1653 | 0.1658 | 0.7287 | 0.1344 | 0.0008 | 0.7039 | -0.0861 | 0.5637 | 24.1753 | 39.2581 | 49.4214 | 8 | 5.1941 | 1.2983 | -1.0857 | 6.629 | -0.9172 | 0.3839 | 0.2521 | -0.4151 | 0.7053 | 0.4827 | -0.2215 | -0.4068 | -0.2917 | 0.5028 | -0.1019 | 0.5643 | 0.1724 | -0.0676 | 0.6869 | -0.0292 | 0.5517 | 42.5552 | 33.6376 | 46.4059 | 9 | 3.127 | -0.8611 | -1.4413 | 3.9214 | 0.26 | 3.9394 | -0.1479 | 1.1718 | -0.1903 | -0.6588 | -0.1867 | 0.7 | -0.1184 | -0.6321 | 0.3486 | 0.8881 | 0.1738 | -0.086 | 0.8605 | -0.202 | 0.6588 | 25.0838 | 12.8234 | 13.5091 | 10 | 5.4298 | -3.6251 | -4.1469 | 9.7507 | 5.5591 | 6.4526 | 0.0736 | 0.5521 | -0.0098 | -0.2461 | -0.866 | 2.0382 | -0.4046 | -1.5844 | 0.7606 | 0.5614 | 0.0481 | -0.1729 | 0.895 | 0.0271 | 1.1344 | -4.6327 | 21.7621 | 30.8702 | 11 | 7.02 | 2.9461 | -2.4815 | 7.3106 | -0.7148 | 4.1394 | 0.3899 | -0.1398 | 0.0326 | 0.587 | -0.2405 | 0.8919 | 0.1118 | -0.2849 | -0.1493 | 0.5134 | 0.0963 | -0.0082 | 0.7201 | -0.071 | 0.7483 | 2.9099 | 22.1275 | 42.3362 | 12 | 2.2364 | 0.0184 | -0.0951 | 2.5979 | -1.5196 | 2.7416 | 0.2417 | 0.4453 | -0.1175 | 0.0369 | -0.1649 | 0.4806 | -0.0513 | -0.4608 | -0.0676 | 0.5672 | 0.1123 | -0.0353 | 0.662 | -0.1271 | 0.6517 | 10.3481 | 23.2722 | 32.5438 | 13 | 7.5033 | 5.1902 | 5.5386 | 4.336 | 4.9595 | 5.704 | 0.1379 | -0.5835 | 0.5473 | 0.8592 | -0.6194 | 0.842 | 0.5604 | -0.5803 | 0.3807 | 0.7852 | 0.0592 | 0.0415 | 0.7844 | 0.0458 | 0.6803 | 27.9894 | 2.3574 | 48.8045 | 14 | 7.3986 | 1.5529 | -0.15 | 4.9968 | 1.5362 | 3.8829 | -0.1099 | 1.2073 | 0.022 | -0.3556 | -0.0616 | 0.3159 | 0.7844 | -0.0798 | 0.1704 | 0.9823 | 0.182 | 0.0085 | 1.0135 | -0.0569 | 0.678 | 32.0955 | -18.5121 | 17.2303 | 15 | 1.3019 | -1.444 | 0.9956 | 3.264 | -0.1027 | 3.3149 | 0.0275 | 0.3809 | -0.3027 | -0.0158 | -0.2507 | 0.5785 | 0.4716 | -0.2939 | 0.2399 | 0.666 | 0.1287 | 0.143 | 0.8967 | -0.0387 | 0.8934 | 34.7413 | -13.2543 | 26.381 | 16 | 4.073 | -0.2377 | -0.8005 | 7.982 | -1.0783 | 8.4087 | -0.5572 | -0.0824 | 0.6646 | 0.0852 | -0.1625 | -0.4311 | -1.0512 | -0.3694 | 0.6804 | 0.7248 | 0.1832 | -0.1276 | 0.796 | 0.0993 | 1.0006 | 54.3024 | 20.0332 | 36.5224 | 17 | 4.8607 | 1.5604 | -1.4744 | 6.1851 | -1.0529 | 5.122 | 0.0647 | -0.8497 | -0.6003 | 1.3286 | -0.2187 | -0.3348 | 0.8753 | 1.2898 | 0.103 | 1.0331 | 0.3792 | 0.1363 | 1.164 | 0.2683 | 0.68 | 49.8003 | -11.6604 | 62.8378 | 18 | 1.4137 | 1.6154 | -1.5587 | 3.1355 | 1.2982 | 8.864 | -0.3118 | -0.5006 | 0.0908 | 0.4048 | -0.2368 | 0.5397 | 1.5387 | 0.3728 | 0.6101 | 0.8175 | 0.229 | 0.0882 | 0.7512 | 0.0812 | 0.8104 | 39.9795 | -9.2952 | 54.4075 | 19 | 1.349 | 0.9122 | -1.3949 | 1.3082 | -0.566 | 1.6218 | -0.0509 | -0.2648 | -0.0701 | 0.0951 | -0.2731 | -0.2564 | 0.2605 | 0.4434 | 0.3519 | 0.7954 | 0.2903 | 0.0557 | 0.6738 | 0.0937 | 0.7469 | 52.1633 | -5.1556 | 47.8727 | 20 | 1.7709 | -0.7116 | -0.1257 | 1.9488 | -0.724 | 2.0616 | -0.7233 | -0.1023 | 0.1338 | 0.5695 | -0.4473 | -0.2424 | 1.0379 | 0.2603 | 1.2886 | 1.0291 | 0.1966 | 0.1764 | 0.7885 | 0.0072 | 0.8387 | 33.9202 | -1.4375 | 60.1087 | 21 | 2.3742 | 2.1144 | -0.2921 | 6.8592 | -4.1411 | 3.0195 | 1.1938 | 0.5725 | -1.1006 | 0.9647 | -0.5222 | -0.1932 | -1.1024 | 0.7072 | -0.8194 | 1.2682 | 0.1373 | -0.1289 | 1.0952 | -0.1473 | 0.7223 | 37.0004 | 8.7076 | 11.2656 | 22 | 7.0137 | -5.3958 | 6.899 | 5.0817 | -6.5786 | 8.556 | -0.1699 | 1.1128 | -0.5835 | -0.3503 | -0.8624 | -0.9066 | -0.0879 | 1.9604 | 0.8369 | 0.9978 | 0.1935 | 0.3252 | 1.0603 | 0.3132 | 1.297 | 71.5821 | 3.2456 | 15.5689 | 23 | 8.3901 | 2.0878 | -1.603 | 0.8925 | 0.5074 | 2.4836 | -0.0255 | 0.0105 | -0.2667 | -0.0087 | -0.1364 | -0.0428 | -0.2905 | 0.2236 | 0.2065 | 0.654 | 0.1315 | 0.0133 | 0.926 | 0.3151 | 0.9516 | 69.5452 | 6.5032 | 28.7205 | 24 | 2.0459 | 0.7942 | -1.1503 | 2.9443 | 0.7331 | 1.107 | 0.08 | 0.5183 | 0.3259 | -0.4951 | -0.15 | -0.5589 | -0.1541 | 0.0169 | 0.067 | 0.7518 | 0.2672 | 0.0917 | 0.8706 | 0.2954 | 0.8357 | 58.8194 | 3.0274 | 23.9457 |
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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 26 ) | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 27 through 95 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 96 through 192 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 193 through 220 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid -5 through 26 ) | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 27 through 95 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 96 through 174 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 175 through 219 )9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid -5 through 25 ) | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 26 through 50 )11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 51 through 95 )12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 96 through 219 )13 | X-RAY DIFFRACTION | 13 | chain 'D' and (resid -5 through 26 ) | 14 | X-RAY DIFFRACTION | 14 | chain 'D' and (resid 27 through 106 )15 | X-RAY DIFFRACTION | 15 | chain 'D' and (resid 107 through 219 )16 | X-RAY DIFFRACTION | 16 | chain 'E' and (resid -5 through 26 ) | 17 | X-RAY DIFFRACTION | 17 | chain 'E' and (resid 27 through 65 )18 | X-RAY DIFFRACTION | 18 | chain 'E' and (resid 66 through 95 )19 | X-RAY DIFFRACTION | 19 | chain 'E' and (resid 96 through 192 )20 | X-RAY DIFFRACTION | 20 | chain 'E' and (resid 193 through 220 )21 | X-RAY DIFFRACTION | 21 | chain 'F' and (resid -5 through 25 ) | 22 | X-RAY DIFFRACTION | 22 | chain 'F' | | | | | | | | | | | | | | | |
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