Software | Name | Version | Classification |
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PHENIX | 1.14_3260refinementPDB_EXTRACT | 3.25 | data extractionXDS | | data reductionAimless | | data scalingMrBUMP | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 0 / Resolution: 1.704→45.976 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.85 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1842 | 1998 | 1.9 % |
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Rwork | 0.1537 | 102920 | - |
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obs | 0.1543 | 104918 | 99.79 % |
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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: 70.45 Å2 / Biso mean: 22.8636 Å2 / Biso min: 8.66 Å2 |
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Refinement step | Cycle: final / Resolution: 1.704→45.976 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6881 | 0 | 30 | 1204 | 8115 |
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Biso mean | - | - | 15.04 | 37.58 | - |
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Num. residues | - | - | - | - | 891 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 7158 | X-RAY DIFFRACTION | f_angle_d0.84 | 9744 | X-RAY DIFFRACTION | f_chiral_restr0.053 | 1065 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1290 | X-RAY DIFFRACTION | f_dihedral_angle_d7.772 | 5769 | | | | | |
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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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1.704-1.7466 | 0.2628 | 142 | 0.2422 | 7142 | 98 | 1.7466-1.7938 | 0.2453 | 133 | 0.2219 | 7266 | 100 | 1.7938-1.8466 | 0.2587 | 136 | 0.2151 | 7293 | 100 | 1.8466-1.9062 | 0.241 | 145 | 0.1999 | 7330 | 100 | 1.9062-1.9744 | 0.2348 | 138 | 0.1694 | 7273 | 100 | 1.9744-2.0534 | 0.1902 | 150 | 0.1604 | 7321 | 100 | 2.0534-2.1469 | 0.1912 | 144 | 0.1538 | 7298 | 100 | 2.1469-2.2601 | 0.1613 | 136 | 0.1484 | 7342 | 100 | 2.2601-2.4016 | 0.2158 | 144 | 0.1507 | 7329 | 100 | 2.4016-2.5871 | 0.1842 | 145 | 0.1522 | 7345 | 100 | 2.5871-2.8474 | 0.1835 | 140 | 0.1569 | 7419 | 100 | 2.8474-3.2593 | 0.1643 | 143 | 0.1503 | 7408 | 100 | 3.2593-4.106 | 0.1495 | 149 | 0.124 | 7494 | 100 | 4.106-45.97 | 0.1686 | 153 | 0.1382 | 7660 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -10.7657 Å / Origin y: 39.8707 Å / Origin z: 26.0091 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0925 Å2 | -0.024 Å2 | -0 Å2 | - | 0.1139 Å2 | -0.0033 Å2 | - | - | 0.084 Å2 |
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L | 0.4348 °2 | -0.3443 °2 | -0.0917 °2 | - | 0.8771 °2 | 0.1591 °2 | - | - | 0.2859 °2 |
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S | 0.0073 Å ° | -0.0018 Å ° | 0.0589 Å ° | -0.0438 Å ° | 0.0084 Å ° | -0.053 Å ° | -0.0169 Å ° | 0.0369 Å ° | -0.013 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 | allA0 - 445 | 2 | X-RAY DIFFRACTION | 1 | allE2 - 3 | 3 | X-RAY DIFFRACTION | 1 | allB1 - 445 | 4 | X-RAY DIFFRACTION | 1 | allS1 - 1235 | | | | | | | | |
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