Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE)refinementMOSFLM | | data reductionSCALA | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→53.678 Å / σ(F): 1.34 / Phase error: 17.04 / Stereochemistry target values: TWIN_LSQ_F
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1749 | 3737 | 5 % |
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Rwork | 0.1371 | - | - |
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obs | 0.1384 | 74256 | 99.99 % |
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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 mean: 27.5 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.65→53.678 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10381 | 0 | 0 | 1712 | 12093 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 10751 | X-RAY DIFFRACTION | f_angle_d0.96 | 14771 | X-RAY DIFFRACTION | f_dihedral_angle_d14.075 | 3801 | X-RAY DIFFRACTION | f_chiral_restr0.068 | 1713 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1960 | | | | | |
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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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2.6502-2.6959 | 0.2481 | 192 | 0.1687 | 3484 | X-RAY DIFFRACTION | 95 | 2.6959-2.7449 | 0.2406 | 187 | 0.1604 | 3560 | X-RAY DIFFRACTION | 95 | 2.7449-2.7977 | 0.2079 | 180 | 0.1559 | 3497 | X-RAY DIFFRACTION | 95 | 2.7977-2.8547 | 0.2391 | 176 | 0.1558 | 3531 | X-RAY DIFFRACTION | 95 | 2.8547-2.9168 | 0.2017 | 205 | 0.1496 | 3481 | X-RAY DIFFRACTION | 94 | 2.9168-2.9846 | 0.1967 | 192 | 0.1513 | 3510 | X-RAY DIFFRACTION | 95 | 2.9846-3.0592 | 0.1999 | 190 | 0.1447 | 3548 | X-RAY DIFFRACTION | 95 | 3.0592-3.1419 | 0.2003 | 189 | 0.1385 | 3476 | X-RAY DIFFRACTION | 95 | 3.1419-3.2343 | 0.1847 | 171 | 0.1335 | 3550 | X-RAY DIFFRACTION | 95 | 3.2343-3.3386 | 0.1657 | 179 | 0.1377 | 3517 | X-RAY DIFFRACTION | 95 | 3.3386-3.4578 | 0.1485 | 185 | 0.1338 | 3516 | X-RAY DIFFRACTION | 95 | 3.4578-3.5962 | 0.1679 | 188 | 0.1251 | 3531 | X-RAY DIFFRACTION | 95 | 3.5962-3.7597 | 0.1494 | 188 | 0.1182 | 3537 | X-RAY DIFFRACTION | 95 | 3.7597-3.9576 | 0.1585 | 204 | 0.1157 | 3519 | X-RAY DIFFRACTION | 95 | 3.9576-4.2053 | 0.157 | 166 | 0.1104 | 3509 | X-RAY DIFFRACTION | 95 | 4.2053-4.5294 | 0.1507 | 207 | 0.1113 | 3507 | X-RAY DIFFRACTION | 94 | 4.5294-4.9841 | 0.1391 | 181 | 0.1149 | 3544 | X-RAY DIFFRACTION | 95 | 4.9841-5.7029 | 0.1536 | 176 | 0.1307 | 3526 | X-RAY DIFFRACTION | 95 | 5.7029-7.1757 | 0.1935 | 190 | 0.1622 | 3551 | X-RAY DIFFRACTION | 95 | 7.1757-35.9916 | 0.172 | 191 | 0.1747 | 3590 | X-RAY DIFFRACTION | 95 |
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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 | 3.772 | -0.1029 | -1.3697 | 1.7912 | 0.499 | 2.7732 | 0.1838 | 0.1393 | 0.1442 | -0.1374 | 0.1211 | -0.2104 | -0.4893 | 0.2528 | -0.2381 | 0.2154 | -0.0928 | -0.0679 | 0.2345 | -0.0321 | 0.2115 | 50.1521 | 48.886 | -8.8931 | 2 | 4.3527 | 4.8425 | 5.2951 | 6.3473 | 5.548 | 7.3369 | 0.4135 | -0.621 | 0.5332 | 0.5005 | -0.4533 | 0.0536 | 0.4062 | -0.4635 | 0.0743 | 0.1155 | -0.0363 | 0.0622 | 0.2996 | -0.0475 | 0.2846 | 26.1622 | 34.4154 | -5.3073 | 3 | 0.7927 | 0.0674 | -0.1514 | 3.1189 | -0.3347 | 0.948 | 0.0273 | 0.2146 | -0.0333 | -0.4776 | 0.0011 | -0.0015 | 0.0935 | 0.0964 | 0.0034 | 0.1907 | -0.0256 | -0.0278 | 0.1824 | -0.0414 | 0.1106 | 39.4376 | 30.7254 | -28.7105 | 4 | 0.1775 | 0.0667 | -0.0075 | 1.6538 | 1.0559 | 1.0448 | -0.0214 | -0.076 | 0.1029 | 0.1799 | 0.0718 | -0.1205 | 0.1264 | 0.1361 | -0.0586 | 0.1397 | -0.0268 | -0.0482 | 0.1631 | -0.007 | 0.1413 | 43.8331 | 31.0582 | -9.3125 | 5 | 1.7371 | 1.2328 | -0.63 | 4.5724 | -0.1252 | 1.9551 | 0.0633 | 0.0502 | -0.2727 | 0.3549 | -0.0794 | -0.3289 | 0.3364 | 0.2954 | 0.0391 | 0.15 | 0.0435 | -0.0574 | 0.1896 | -0.0144 | 0.1316 | 47.5041 | 24.5738 | -10.2463 | 6 | 1.3805 | -0.4101 | 0.301 | 1.9642 | 0.1884 | 2.3425 | 0.09 | -0.0323 | 0.0368 | -0.0033 | -0.0564 | -0.2908 | -0.1069 | 0.2949 | -0.0314 | 0.1079 | -0.0684 | -0.0185 | 0.2144 | -0.0296 | 0.1735 | 50.164 | 39.236 | -14.9782 | 7 | 2.2688 | -0.7895 | 1.8271 | 2.9743 | -3.2004 | 6.6152 | 0.0971 | 0.2067 | -0.2384 | -0.221 | -0.3496 | -0.0662 | 0.5513 | 0.6175 | -0.1221 | 0.304 | -0.0657 | -0.035 | 0.1638 | -0.1272 | 0.125 | 44.4938 | 35.1152 | 17.6514 | 8 | 1.075 | 0.6587 | 0.364 | 5.0576 | 1.6335 | 2.1086 | 0.129 | -0.2367 | -0.1035 | 0.5674 | -0.0441 | -0.1172 | 0.0131 | -0.1483 | -0.1108 | 0.2379 | 0.0104 | -0.0643 | 0.2445 | 0.0172 | 0.1539 | 48.4369 | 43.5159 | 42.3381 | 9 | 1.5509 | -1 | -0.535 | 2.7907 | 1.0224 | 0.965 | -0.071 | 0.0027 | 0.2689 | -0.0117 | -0.0223 | -0.3103 | -0.2897 | 0.3308 | -0.0441 | 0.2092 | -0.0802 | -0.084 | 0.1762 | 0.0084 | 0.1987 | 59.993 | 58.748 | 24.5626 | 10 | 0.6469 | -0.4689 | 0.3616 | 1.5071 | 0.3555 | 0.8842 | 0.0022 | -0.0539 | 0.0746 | 0.1071 | -0.0284 | -0.0394 | -0.1179 | -0.0316 | 0.0253 | 0.1508 | -0.0458 | -0.0346 | 0.1223 | -0.0193 | 0.1089 | 44.6068 | 56.9054 | 27.113 | 11 | 0.8603 | -0.3562 | -1.0333 | 4.2775 | 1.4404 | 1.6166 | 0.1171 | 0.1692 | 0.1138 | 0.0549 | 0.0018 | 0.2062 | -0.0628 | -0.2719 | -0.0184 | 0.1131 | -0.0358 | -0.0687 | 0.1659 | 0.0068 | 0.1282 | 36.8877 | 57.6142 | 25.641 | 12 | 1.5162 | -0.2475 | 0.1241 | 1.9785 | -0.649 | 1.3582 | 0.0517 | -0.0362 | -0.0607 | -0.104 | -0.0649 | 0.0135 | 0.024 | -0.0371 | 0.0053 | 0.1526 | -0.0588 | -0.0267 | 0.1171 | -0.0484 | 0.121 | 46.2184 | 46.298 | 20.6106 | 13 | 2.1491 | 0.5495 | -0.6172 | 1.8345 | 0.8933 | 3.1173 | 0.0015 | -0.1252 | 0.1815 | 0.0355 | 0.0333 | -0.2041 | -0.2341 | 0.3958 | -0.0839 | 0.1694 | 0.0079 | -0.0453 | 0.1324 | -0.0189 | 0.1969 | 18.9835 | 55.9862 | -23.6503 | 14 | 3.9412 | -0.5669 | 1.5821 | 0.7499 | 0.282 | 1.2968 | 0.0032 | -0.0276 | -0.4628 | 0.0954 | -0.0118 | 0.1434 | 0.1743 | 0.0274 | -0.0279 | 0.1415 | -0.0379 | 0.0293 | 0.1337 | -0.0594 | 0.2345 | 9.1402 | 33.9549 | -19.1653 | 15 | 2.099 | 0.5185 | -0.3501 | 1.0137 | -0.1843 | 1.3241 | -0.0148 | -0.0238 | 0.02 | 0.0159 | 0.0271 | -0.0122 | -0.092 | -0.1159 | -0.0105 | 0.1261 | 0.0103 | -0.0016 | 0.1088 | -0.0643 | 0.1198 | 2.7074 | 47.938 | -21.4307 | 16 | 2.4734 | 1.3179 | 0.8336 | 1.3423 | -0.3294 | 2.4376 | -0.0038 | -0.0837 | 0.3481 | 0.1494 | 0.0116 | 0.0997 | -0.3176 | -0.3319 | -0.0423 | 0.1939 | 0.0466 | 0.0294 | 0.1241 | -0.074 | 0.2091 | -1.8175 | 54.3538 | -20.151 | 17 | 1.645 | 0.3942 | -0.3307 | 1.4406 | -0.2539 | 1.6818 | 0.1236 | -0.2486 | 0.0977 | 0.0368 | -0.1277 | 0.0004 | -0.1879 | 0.0038 | 0.0175 | 0.1911 | -0.0356 | -0.0305 | 0.1325 | -0.0716 | 0.1564 | 12.7388 | 52.1551 | -15.1017 | 18 | 2.3716 | -0.2087 | 0.9414 | 1.5398 | 0.0699 | 1.2931 | -0.0885 | 0.0816 | 0.363 | -0.5095 | 0.0337 | 0.5062 | -0.2594 | -0.297 | 0.0542 | 0.4022 | 0.0546 | -0.1309 | 0.3138 | 0.0521 | 0.3495 | 23.1435 | 99.8133 | 13.1366 | 19 | 1.7946 | -1.0318 | -0.5082 | 3.2252 | 0.7108 | 1.3003 | -0.0435 | -0.1262 | -0.1321 | 0.314 | 0.0321 | 0.1679 | 0.0685 | -0.0519 | 0.0076 | 0.1435 | -0.0261 | -0.0203 | 0.1538 | 0.0147 | 0.1086 | 34.4721 | 90.0712 | 34.1403 | 20 | 1.0001 | -0.2374 | -0.0708 | 1.7616 | -0.0142 | 1.4235 | -0.0079 | 0.2044 | -0.0222 | -0.5638 | 0.0217 | 0.4218 | 0.0051 | -0.22 | -0.0331 | 0.2829 | -0.0265 | -0.1258 | 0.2279 | -0.0068 | 0.2499 | 27.6261 | 87.2457 | 16.7452 |
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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 0 THROUGH 42 )2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESID 43 THROUGH 58 )3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESID 59 THROUGH 166 )4 | X-RAY DIFFRACTION | 4 | CHAIN A AND (RESID 167 THROUGH 249 )5 | X-RAY DIFFRACTION | 5 | CHAIN A AND (RESID 250 THROUGH 285 )6 | X-RAY DIFFRACTION | 6 | CHAIN A AND (RESID 286 THROUGH 337 )7 | X-RAY DIFFRACTION | 7 | CHAIN B AND (RESID 1 THROUGH 31 )8 | X-RAY DIFFRACTION | 8 | CHAIN B AND (RESID 32 THROUGH 58 )9 | X-RAY DIFFRACTION | 9 | CHAIN B AND (RESID 59 THROUGH 128 )10 | X-RAY DIFFRACTION | 10 | CHAIN B AND (RESID 129 THROUGH 249 )11 | X-RAY DIFFRACTION | 11 | CHAIN B AND (RESID 250 THROUGH 285 )12 | X-RAY DIFFRACTION | 12 | CHAIN B AND (RESID 286 THROUGH 337 )13 | X-RAY DIFFRACTION | 13 | CHAIN C AND (RESID 1 THROUGH 58 )14 | X-RAY DIFFRACTION | 14 | CHAIN C AND (RESID 59 THROUGH 128 )15 | X-RAY DIFFRACTION | 15 | CHAIN C AND (RESID 129 THROUGH 249 )16 | X-RAY DIFFRACTION | 16 | CHAIN C | | | | | | | | | | | | | | | |
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