Software | Name | Version | Classification |
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HKL-2000 | | data scalingPHENIX | 1.11.1_2575refinementPDB_EXTRACT | 3.24 | data extractionHKL-2000 | | data reductionPHASER | | phasing | | | | | |
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Refinement | Resolution: 1.799→38.129 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.93
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.204 | 930 | 5.1 % |
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Rwork | 0.1798 | - | - |
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obs | 0.181 | 18222 | 99.28 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 89.49 Å2 / Biso mean: 23.6151 Å2 / Biso min: 10.07 Å2 |
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Refinement step | Cycle: final / Resolution: 1.799→38.129 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1320 | 0 | 0 | 208 | 1528 |
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Biso mean | - | - | - | 35.38 | - |
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Num. residues | - | - | - | - | 162 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 1374 | X-RAY DIFFRACTION | f_angle_d0.697 | 1877 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 199 | X-RAY DIFFRACTION | f_plane_restr0.004 | 241 | X-RAY DIFFRACTION | f_dihedral_angle_d16.621 | 482 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.7988-1.8936 | 0.3767 | 122 | 0.3567 | 2355 | 2477 | 96 | 1.8936-2.0122 | 0.2127 | 147 | 0.196 | 2404 | 2551 | 99 | 2.0122-2.1676 | 0.1513 | 98 | 0.1669 | 2455 | 2553 | 100 | 2.1676-2.3857 | 0.1913 | 141 | 0.1611 | 2472 | 2613 | 100 | 2.3857-2.7308 | 0.2159 | 139 | 0.1799 | 2459 | 2598 | 100 | 2.7308-3.4402 | 0.1929 | 129 | 0.1692 | 2523 | 2652 | 100 | 3.4402-38.1376 | 0.199 | 154 | 0.1701 | 2624 | 2778 | 100 |
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Refinement TLS params. | Method: refined / Origin x: 39.6356 Å / Origin y: 55.8409 Å / Origin z: 139.6974 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1256 Å2 | 0.0063 Å2 | -0.0006 Å2 | - | 0.1232 Å2 | -0.0046 Å2 | - | - | 0.1326 Å2 |
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L | 0.4528 °2 | -0.1053 °2 | -0.0914 °2 | - | 0.4681 °2 | 0.189 °2 | - | - | 0.8616 °2 |
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S | 0.0041 Å ° | 0.0163 Å ° | -0.0043 Å ° | 0.0336 Å ° | -0.0021 Å ° | -0.0015 Å ° | 0.0232 Å ° | 0.0086 Å ° | -0 Å ° |
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Refinement TLS group | Selection details: all |
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