Software | Name | Version | Classification |
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PHENIX | 1.12_2829refinementHKL-2000 | | data scalingPDB_EXTRACT | 3.25 | data extractionHKL-2000 | | data reductionPHENIX | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1e7s Resolution: 2.05→49.549 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.22 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2135 | 1859 | 3.99 % |
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Rwork | 0.1654 | 44789 | - |
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obs | 0.1673 | 46648 | 98.95 % |
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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 max: 135.92 Å2 / Biso mean: 31.0493 Å2 / Biso min: 14.1 Å2 |
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Refinement step | Cycle: final / Resolution: 2.05→49.549 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5570 | 0 | 96 | 544 | 6210 |
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Biso mean | - | - | 36.81 | 35.23 | - |
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Num. residues | - | - | - | - | 696 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 5785 | X-RAY DIFFRACTION | f_angle_d0.975 | 7802 | X-RAY DIFFRACTION | f_chiral_restr0.057 | 846 | X-RAY DIFFRACTION | f_plane_restr0.006 | 988 | X-RAY DIFFRACTION | f_dihedral_angle_d16.679 | 3414 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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2.05-2.1054 | 0.2653 | 143 | 0.1944 | 3422 | 99 | 2.1054-2.1674 | 0.2579 | 142 | 0.185 | 3481 | 100 | 2.1674-2.2373 | 0.2257 | 141 | 0.1709 | 3398 | 99 | 2.2373-2.3173 | 0.2199 | 143 | 0.1732 | 3450 | 99 | 2.3173-2.4101 | 0.2202 | 144 | 0.1677 | 3450 | 99 | 2.4101-2.5198 | 0.2136 | 143 | 0.1724 | 3397 | 98 | 2.5198-2.6526 | 0.2338 | 143 | 0.1741 | 3467 | 100 | 2.6526-2.8188 | 0.2358 | 137 | 0.1802 | 3458 | 99 | 2.8188-3.0364 | 0.2208 | 152 | 0.1768 | 3453 | 99 | 3.0364-3.3419 | 0.2029 | 140 | 0.1743 | 3415 | 98 | 3.3419-3.8253 | 0.1897 | 144 | 0.1448 | 3466 | 100 | 3.8253-4.8189 | 0.1752 | 139 | 0.1432 | 3432 | 98 | 4.8189-49.549 | 0.2275 | 148 | 0.1662 | 3500 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -3.2129 Å / Origin y: 58.9476 Å / Origin z: 45.0395 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1739 Å2 | 0.009 Å2 | 0.0073 Å2 | - | 0.2007 Å2 | 0.006 Å2 | - | - | 0.194 Å2 |
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L | 0.3288 °2 | 0.0199 °2 | 0.147 °2 | - | 0.1437 °2 | 0.0529 °2 | - | - | 0.4818 °2 |
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S | -0.01 Å ° | -0.0012 Å ° | 0.0201 Å ° | 0.0193 Å ° | -0.0055 Å ° | 0.0012 Å ° | -0.0028 Å ° | 0.0284 Å ° | 0.0231 Å ° |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | allA-1 - 350 | 2 | X-RAY DIFFRACTION | 1 | allB-1 - 350 | 3 | X-RAY DIFFRACTION | 1 | allS1 - 544 | | | | | | |
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