Software | Name | Version | Classification |
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PHENIX | (1.20.1_4487: ???)refinementXDS | | data scalingXDS | | data reductionPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→49.35 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.93 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2554 | 2047 | 5 % |
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Rwork | 0.206 | - | - |
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obs | 0.2085 | 40926 | 99.24 % |
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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: 2.66→49.35 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 8800 | 0 | 135 | 158 | 9093 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 9089 | X-RAY DIFFRACTION | f_angle_d0.502 | 12309 | X-RAY DIFFRACTION | f_dihedral_angle_d15.92 | 3422 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 1388 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1564 | | | | | |
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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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2.66-2.72 | 0.3798 | 132 | 0.3114 | 2507 | X-RAY DIFFRACTION | 98 | 2.72-2.79 | 0.3475 | 133 | 0.2943 | 2529 | X-RAY DIFFRACTION | 98 | 2.79-2.87 | 0.2913 | 134 | 0.2801 | 2551 | X-RAY DIFFRACTION | 100 | 2.87-2.95 | 0.3618 | 135 | 0.2798 | 2562 | X-RAY DIFFRACTION | 98 | 2.95-3.05 | 0.3623 | 135 | 0.2718 | 2566 | X-RAY DIFFRACTION | 100 | 3.05-3.16 | 0.3375 | 133 | 0.2696 | 2533 | X-RAY DIFFRACTION | 99 | 3.16-3.28 | 0.3512 | 136 | 0.2447 | 2582 | X-RAY DIFFRACTION | 99 | 3.28-3.43 | 0.2897 | 136 | 0.2162 | 2584 | X-RAY DIFFRACTION | 99 | 3.43-3.61 | 0.2478 | 137 | 0.2011 | 2591 | X-RAY DIFFRACTION | 100 | 3.61-3.84 | 0.2493 | 136 | 0.1862 | 2586 | X-RAY DIFFRACTION | 99 | 3.84-4.14 | 0.2207 | 137 | 0.1649 | 2602 | X-RAY DIFFRACTION | 100 | 4.14-4.55 | 0.1649 | 137 | 0.1467 | 2608 | X-RAY DIFFRACTION | 99 | 4.55-5.21 | 0.203 | 139 | 0.1539 | 2641 | X-RAY DIFFRACTION | 100 | 5.21-6.56 | 0.2532 | 139 | 0.2122 | 2630 | X-RAY DIFFRACTION | 98 | 6.56-49.35 | 0.2333 | 148 | 0.2026 | 2807 | 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 | 2.9028 | 0.4142 | 1.4263 | 2.9882 | 1.0679 | 2.0019 | -0.3477 | 0.3543 | 0.2365 | -0.2229 | -0.4507 | -0.1116 | -0.1678 | 0.7901 | 0.7236 | 0.5969 | -0.049 | -0.0764 | 0.6575 | 0.0608 | 0.4593 | 6.6296 | 21.0369 | -23.1838 | 2 | 1.9401 | 0.2115 | 1.0178 | 1.7009 | 0.84 | 7.6122 | 0.0606 | -0.1511 | 0.1858 | 0.1491 | 0.1078 | -0.2463 | 0.1207 | -0.5549 | 0.1197 | 0.34 | 0.0551 | -0.0536 | 0.3183 | 0.0116 | 0.4095 | 9.4414 | 23.1614 | 8.9129 | 3 | 2.137 | 0.7086 | -1.0998 | 1.0564 | -0.9682 | 3.9596 | 0.5501 | 0.1305 | 0.3017 | 0.3574 | 0.2631 | 0.1497 | -0.431 | -0.2268 | -0.6466 | 0.6899 | 0.0183 | -0.0294 | 0.5764 | -0.061 | 0.4081 | 6.6054 | 30.1686 | 18.5383 | 4 | 1.519 | 0.115 | 0.039 | 1.3149 | -0.5908 | 2.3748 | 0.0058 | -0.096 | 0.136 | -0.01 | -0.0554 | 0.179 | -0.1179 | -0.2651 | 0.0538 | 0.4802 | 0.045 | -0.0555 | 0.4504 | -0.0404 | 0.4798 | -0.7698 | 23.9314 | 8.2944 | 5 | 1.3574 | 0.3466 | 0.3071 | 0.6672 | -0.8006 | 1.8575 | -0.0068 | -0.1427 | -0.1441 | -0.2743 | 0.0509 | 0.1036 | 0.107 | -0.3277 | -0.0478 | 0.4605 | -0.0152 | -0.0792 | 0.4009 | -0.0602 | 0.3687 | 3.0612 | 15.2451 | 10.0314 | 6 | 3.7282 | 4.4742 | -0.5717 | 5.471 | -0.0892 | 2.1362 | 0.173 | -0.1185 | -0.8836 | 0.4975 | -0.2612 | -0.387 | 0.4561 | 0.3631 | -0.0497 | 0.5498 | 0.1123 | -0.0628 | 0.4295 | -0.0586 | 0.5371 | 15.05 | 2.8171 | 17.0019 | 7 | 4.8952 | -1.302 | -1.9116 | 2.9086 | -1.0323 | 4.6133 | -0.0341 | 0.8263 | -0.7144 | -0.3421 | -0.3942 | -0.0826 | 0.0893 | -0.2181 | 0.3915 | 0.528 | -0.0718 | -0.0218 | 0.4758 | -0.0957 | 0.4808 | 9.7792 | 3.2717 | -0.2134 | 8 | 1.3201 | -1.5603 | 2.1645 | 8.2649 | 1.5674 | 6.2969 | 0.0735 | 0.7063 | 0.1503 | -0.0792 | -0.0395 | -0.9215 | -0.7035 | 0.0068 | -0.0717 | 0.3607 | -0.0103 | 0.0156 | 0.4984 | -0.0204 | 0.3882 | 27.0524 | 23.4539 | 10.4282 | 9 | 4.1314 | -0.9213 | 1.5496 | 0.8244 | -0.1931 | 2.261 | 0.7285 | 0.4595 | -0.4276 | 0.0831 | -0.3125 | -0.0717 | 0.2259 | 0.1793 | -0.3617 | 0.5318 | 0.0012 | -0.027 | 0.3497 | 0.0298 | 0.3566 | 9.983 | 15.0526 | 3.3689 | 10 | 4.944 | -0.6117 | -0.5465 | 2.1861 | -0.6379 | 2.7179 | -0.3886 | -0.5415 | 0.1143 | 0.0049 | 0.0899 | -0.3074 | 0.1418 | 0.0274 | 0.2974 | 0.5177 | 0.012 | -0.132 | 0.4762 | 0.0262 | 0.4207 | 20.0459 | 7.9113 | 41.2872 | 11 | 1.3115 | 0.0074 | 0.4776 | 3.019 | -1.249 | 6.5796 | -0.0319 | -0.2979 | -0.0814 | 0.1936 | -0.3356 | -0.4869 | 0.2048 | 0.3495 | 0.2541 | 0.4631 | -0.0416 | -0.0917 | 0.4639 | 0.0484 | 0.5715 | 12.6628 | 9.9913 | 47.2235 | 12 | 1.0236 | -0.0417 | -1.1617 | 0.2032 | 0.5725 | 3.9274 | 0.0249 | -0.2331 | 0.1237 | 0.1236 | -0.0571 | -0.1372 | -0.2793 | 0.4274 | 0.0184 | 0.4291 | -0.018 | -0.1025 | 0.3596 | 0.0019 | 0.3983 | 21.5376 | 20.6822 | 41.0633 | 13 | 0.6437 | 0.1208 | -0.9528 | 0.3057 | -0.0441 | 3.2284 | 0.1546 | 0.0623 | 0.1321 | 0.0532 | 0.0572 | -0.0007 | -0.3745 | 0.0973 | -0.2138 | 0.4316 | 0.0084 | 0.0727 | 0.372 | 0.0139 | 0.4189 | -20.2951 | -12.1925 | 46.5683 | 14 | 1.8436 | -0.109 | 0.2681 | 0.8329 | 0.3802 | 4.7012 | -0.0796 | -0.0925 | -0.1167 | 0.157 | 0.0762 | 0.0732 | 0.642 | -0.4152 | -0.0101 | 0.4502 | -0.0477 | 0.0846 | 0.4337 | 0.0648 | 0.4253 | -24.0334 | -25.1998 | 39.3931 | 15 | 3.512 | 1.1408 | -0.3214 | 2.1888 | -0.2382 | 1.247 | 0.1241 | -0.1147 | -0.2132 | 0.217 | -0.0901 | 0.3443 | 0.528 | -0.3403 | -0.0636 | 0.4599 | -0.0869 | 0.0597 | 0.4885 | -0.0129 | 0.4555 | -8.4914 | -28.9789 | 9.1328 | 16 | 4.2696 | -0.0389 | 1.2698 | 6.5031 | 4.3398 | 3.3302 | -0.0656 | -0.2345 | -0.2838 | -0.043 | -0.4615 | 0.7094 | 0.4589 | -0.4867 | 0.4393 | 0.4186 | -0.061 | 0.0432 | 0.4792 | -0.0649 | 0.4852 | -3.9122 | -27.864 | 9.0681 | 17 | 5.5371 | -0.2423 | -3.8886 | 1.9146 | -1.2418 | 8.2061 | -0.2951 | -0.6405 | -0.0266 | 0.0557 | -0.3625 | -0.1248 | 0.1297 | 1.1992 | 0.5506 | 0.418 | -0.0797 | 0.05 | 0.5251 | 0.0993 | 0.4941 | 7.5728 | -20.477 | 9.373 | 18 | 4.2847 | 0.465 | -1.2254 | 1.2843 | -0.1294 | 2.1142 | 0.0532 | 0.415 | 0.1407 | -0.2079 | 0.0735 | -0.0716 | 0.0505 | -0.2366 | -0.1347 | 0.4263 | 0.0033 | 0.042 | 0.4062 | 0.0357 | 0.3458 | -12.3839 | -16.7085 | 9.6657 | 19 | 8.48 | 1.1149 | -1.9397 | 1.2375 | 0.1417 | 3.4443 | 0.0187 | 1.1281 | -0.0226 | -0.2477 | 0.0897 | 0.0243 | 0.4261 | -0.2207 | -0.1071 | 0.4957 | 0.0416 | 0.0278 | 0.4783 | 0.0155 | 0.3513 | -6.4385 | -16.5487 | -0.2789 |
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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 12 through 29 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 30 through 52 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 53 through 75 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 76 through 129 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 130 through 185 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 186 through 203 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 204 through 229 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 230 through 252 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 253 through 302 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 118 through 182 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 183 through 237 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 238 through 409 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 12 through 158 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 159 through 302 )15 | X-RAY DIFFRACTION | 15 | chain 'D' and (resid 118 through 182 )16 | X-RAY DIFFRACTION | 16 | chain 'D' | | | | | | | | | | | | | | | |
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