Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementiMOSFLM | | data reductionAimless | | data scalingPHENIX | | phasing | | | | |
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Refinement | Resolution: 2.334→39.354 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.43 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2594 | 1538 | 10 % |
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Rwork | 0.2277 | - | - |
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obs | 0.2309 | 15374 | 96.06 % |
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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: 2.334→39.354 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2424 | 0 | 39 | 267 | 2730 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.012 | 2490 | X-RAY DIFFRACTION | f_angle_d1.691 | 3330 | X-RAY DIFFRACTION | f_dihedral_angle_d19.722 | 990 | X-RAY DIFFRACTION | f_chiral_restr0.064 | 348 | X-RAY DIFFRACTION | f_plane_restr0.007 | 426 | | | | | |
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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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2.334-2.4093 | 0.2978 | 131 | 0.2571 | 1179 | X-RAY DIFFRACTION | 91 | 2.4093-2.4954 | 0.2875 | 142 | 0.2582 | 1270 | X-RAY DIFFRACTION | 97 | 2.4954-2.5953 | 0.2885 | 139 | 0.2646 | 1261 | X-RAY DIFFRACTION | 97 | 2.5953-2.7134 | 0.3116 | 141 | 0.2597 | 1263 | X-RAY DIFFRACTION | 97 | 2.7134-2.8564 | 0.2989 | 142 | 0.2607 | 1279 | X-RAY DIFFRACTION | 98 | 2.8564-3.0353 | 0.3054 | 141 | 0.2427 | 1270 | X-RAY DIFFRACTION | 97 | 3.0353-3.2696 | 0.2609 | 141 | 0.23 | 1263 | X-RAY DIFFRACTION | 97 | 3.2696-3.5984 | 0.26 | 139 | 0.2069 | 1254 | X-RAY DIFFRACTION | 97 | 3.5984-4.1186 | 0.2113 | 141 | 0.1942 | 1279 | X-RAY DIFFRACTION | 96 | 4.1186-5.1872 | 0.2198 | 141 | 0.1856 | 1259 | X-RAY DIFFRACTION | 96 | 5.1872-39.3598 | 0.2438 | 140 | 0.2516 | 1259 | X-RAY DIFFRACTION | 93 |
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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 | 1.5258 | -0.9077 | -0.4996 | 1.2216 | 0.974 | 1.5351 | -0.3127 | 0.3476 | -0.793 | 0.1204 | 0.2395 | 0.029 | 0.5631 | 0.0261 | 0.0427 | 0.3809 | 0.1401 | 0.3132 | -0.0135 | -0.0724 | 0.4411 | -7.0257 | 18.4204 | 9.1682 | 2 | 6.5203 | -3.4803 | 2.9866 | 4.377 | -0.9629 | 1.5617 | -0.193 | -0.2692 | -1.2713 | -0.0803 | 0.0364 | 0.5564 | 0.2521 | -0.065 | -0.0513 | 0.6067 | -0.1687 | 0.1289 | 0.2384 | -0.1009 | 0.2826 | -15.8526 | 16.3991 | 11.9314 | 3 | 5.4628 | 1.7118 | -1.9929 | 5.0552 | 1.2562 | 6.9502 | -0.2737 | 0.5523 | 0.2002 | -0.4415 | -0.1716 | 0.7828 | 0.5478 | -0.8134 | 0.2531 | 0.3492 | 0.0773 | -0.1464 | 0.1028 | 0.111 | 0.1725 | -16.7996 | 24.561 | 5.0914 | 4 | 8.7641 | 1.2212 | 0.8481 | 5.4813 | 1.4792 | 7.5653 | 0.1352 | -1.2937 | -0.619 | 1.1462 | -0.6414 | -0.2828 | 1.2208 | 0.0784 | 0.6082 | 0.6088 | 0.0178 | -0.0543 | 0.3191 | 0.1341 | 0.4809 | -14.406 | 23.8247 | 19.6294 | 5 | 3.3057 | -1.4463 | 0.6043 | 4.4888 | -0.2089 | 7.2462 | -0.5145 | -0.2593 | -0.0644 | 0.5987 | 0.062 | 0.134 | 0.1272 | -0.2951 | 0.3473 | 0.2651 | 0.0215 | 0.0461 | 0.0817 | -0.0347 | 0.2234 | -11.7189 | 29.2204 | 15.56 | 6 | 3.2606 | 0.2339 | 1.1222 | 1.3904 | -0.0837 | 1.6259 | -0.0515 | -0.0835 | -0.5338 | 0.0604 | 0.4023 | -0.2024 | 0.2098 | 0.4657 | -0.1485 | 0.3061 | 0.0021 | 0.154 | 0.1335 | -0.0055 | 0.199 | -0.9951 | 25.8271 | 11.0728 | 7 | 4.7438 | 0.4324 | 0.5809 | 1.786 | 0.0866 | 3.6476 | -0.1905 | -0.8895 | 0.0413 | 1.2251 | 0.0971 | 0.8361 | -0.2879 | 0.113 | 0.0873 | 0.4908 | 0.0484 | 0.0777 | 0.3607 | -0.1215 | 0.295 | -12.9814 | 33.0805 | 27.194 | 8 | 2.5218 | -2.1277 | -0.962 | 3.2774 | 3.1929 | 4.6722 | 0.1718 | 0.2991 | -0.2651 | -0.5251 | -0.5165 | 0.3899 | -0.3269 | -0.5556 | 0.3222 | 0.7028 | 0.2526 | 0.0056 | 1.0373 | -0.3602 | 0.5822 | -15.5607 | 27.2671 | 38.1834 | 9 | 2.837 | 1.0721 | -1.9887 | 4.7576 | -1.868 | 5.368 | 0.2812 | 0.3823 | 0.4625 | -0.4609 | 0.2025 | 0.5375 | -0.477 | -0.8211 | -0.4711 | 0.358 | 0.1274 | -0.0215 | 0.1001 | -0.0364 | 0.2823 | -15.8892 | 50.2924 | 7.0237 | 10 | 9.5798 | 2.2033 | 4.1255 | 1.5662 | 1.966 | 5.2597 | -0.7084 | -0.0384 | 0.6398 | 0.3257 | 0.4076 | 0.4486 | -0.416 | 0.0567 | 0.275 | 0.4923 | 0.1088 | 0.1309 | 0.1502 | 0.0136 | 0.3696 | -15.7831 | 58.4094 | 12.5272 | 11 | 3.3279 | -0.0364 | 1.4723 | 3.7704 | -0.7346 | 1.2249 | 0.1795 | -0.3422 | 0.2057 | 0.1247 | -0.2248 | 0.201 | -0.6496 | -1.0034 | 0.0006 | 0.3838 | 0.2246 | 0.0749 | -0.1098 | -0.0403 | 0.2914 | -9.6749 | 48.0388 | 11.3696 | 12 | 8.5944 | -2.4035 | -2.1342 | 1.479 | 1.6976 | 2.0284 | -0.5095 | -1.373 | 0.1725 | 1.2146 | 0.2664 | 0.367 | 0.0561 | 0.143 | 0.1498 | 0.739 | -0.1054 | 0.0156 | 0.4402 | 0.093 | 0.3343 | -9.7457 | 44.9162 | 31.6 | 13 | 7.8091 | -3.5678 | -3.2638 | 5.9051 | 0.0519 | 5.9447 | -0.1282 | 0.0691 | 0.7969 | 0.4976 | 0.0572 | -0.6103 | -0.5128 | 0.4056 | 0.0336 | 0.3349 | -0.1046 | -0.008 | 0.1852 | 0.0239 | 0.3103 | 15.8116 | 42.1719 | 14.6259 | 14 | 3.4635 | -1.8265 | 4.271 | 9.6747 | -1.353 | 9.7274 | -0.6221 | 0.4824 | 0.1212 | -0.3336 | -0.1252 | -1.8341 | -0.7015 | 1.7049 | 0.6763 | 0.3026 | -0.0849 | -0.0031 | 0.6861 | 0.1034 | 0.5187 | 22.5909 | 39.3244 | 20.4427 | 15 | 5.6984 | 0.0736 | -1.2749 | 2.3337 | 0.5607 | 2.6616 | -0.0534 | -0.967 | -0.0348 | 0.9664 | -0.0814 | -0.1304 | 0.1956 | 0.9432 | 0.0716 | 0.4716 | 0.0144 | -0.031 | 0.3241 | -0.0119 | 0.2152 | 14.2879 | 31.9249 | 18.3223 | 16 | 2.6986 | 0.369 | -0.3897 | 5.318 | -0.2574 | 0.7784 | 0.1513 | -0.068 | 0.3832 | -0.1128 | -0.1012 | 0.066 | -0.3462 | 0.1661 | -0.0088 | 0.3215 | -0.0222 | 0.0326 | 0.1189 | -0.0342 | 0.1543 | 6.2414 | 41.5213 | 14.9973 | 17 | 7.5413 | 2.7054 | 2.7333 | 5.0628 | 4.9019 | 4.7545 | -0.0619 | -0.9311 | -0.35 | 1.2125 | -0.0774 | 0.1826 | 0.7113 | 0.0246 | 0.0993 | 0.5468 | 0.0368 | 0.1407 | 0.2676 | -0.0206 | 0.2899 | -0.2914 | 33.3871 | 29.1914 | 18 | 8.2563 | 2.8367 | -5.9604 | 6.9099 | -4.7587 | 1.9996 | -0.1198 | 1.052 | 0.1272 | -1.2795 | 0.1522 | -0.2378 | 0.8661 | -0.9175 | -0.0099 | 1.4176 | 0.049 | -0.0614 | 0.8635 | 0.2352 | 0.4117 | 0.6762 | 36.7748 | 41.8046 |
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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 8 through 24 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 25 through 39 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 40 through 54 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 55 through 63 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 64 through 69 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 70 through 89 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 90 through 101 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 102 through 106 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 8 through 24 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 25 through 38 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 39 through 89 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 90 through 106 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 8 through 24 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 25 through 33 )15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resid 34 through 62 )16 | X-RAY DIFFRACTION | 16 | chain 'C' | | | | | | | | | | | | | | | |
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