Software | Name | Version | Classification |
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PHENIX | 1.13_2998refinementPDB_EXTRACT | 3.24 | data extractionXDS | | data reductionAimless | | data scalingPHASER | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JJE Resolution: 1.969→23.075 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.29
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2743 | 279 | 5.18 % |
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Rwork | 0.2544 | - | - |
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obs | 0.2556 | 5385 | 96.8 % |
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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: 166 Å2 / Biso mean: 75.888 Å2 / Biso min: 34.14 Å2 |
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Refinement step | Cycle: final / Resolution: 1.969→23.075 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 580 | 4 | 2 | 586 |
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Biso mean | - | - | 41.5 | 75.77 | - |
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Num. residues | - | - | - | - | 28 |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.9685-2.4797 | 0.3428 | 127 | 0.3155 | 2557 | 2684 | 98 | 2.4797-23.0767 | 0.2658 | 152 | 0.2452 | 2549 | 2701 | 96 |
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Refinement TLS params. | Method: refined / Origin x: -11.0288 Å / Origin y: -2.4043 Å / Origin z: 9.2058 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.5162 Å2 | -0.0179 Å2 | -0.0244 Å2 | - | 0.4095 Å2 | -0.0355 Å2 | - | - | 0.5747 Å2 |
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L | 5.3135 °2 | 1.0711 °2 | 6.7305 °2 | - | 4.5286 °2 | 0.4859 °2 | - | - | 10.3492 °2 |
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S | -0.5585 Å ° | 0.3055 Å ° | 0.8219 Å ° | -0.7274 Å ° | -0.5979 Å ° | 0.3099 Å ° | -0.3251 Å ° | -0.0055 Å ° | -0.1102 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 | allA1 - 14 | 2 | X-RAY DIFFRACTION | 1 | allB1 - 14 | 3 | X-RAY DIFFRACTION | 1 | allC1 - 3 | 4 | X-RAY DIFFRACTION | 1 | allD1 | 5 | X-RAY DIFFRACTION | 1 | allS1 - 2 | | | | | | | | | | |
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