Software | Name | Version | Classification |
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HKL-2000 | | data collectionHKL-2000 | | data scalingPHENIX | | refinementPDB_EXTRACT | 3.15 | data extractionHKL-2000 | | data reductionPHENIX | | phasing | | | | | |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.002→34.986 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.44 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2024 | 479 | 5.31 % |
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Rwork | 0.1463 | 8547 | - |
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obs | 0.1493 | 9026 | 96.3 % |
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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: 79.63 Å2 / Biso mean: 20.6966 Å2 / Biso min: 7.78 Å2 |
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Refinement step | Cycle: final / Resolution: 2.002→34.986 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1179 | 0 | 43 | 168 | 1390 |
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Biso mean | - | - | 21.34 | 27.92 | - |
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Num. residues | - | - | - | - | 155 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 1256 | X-RAY DIFFRACTION | f_angle_d1.104 | 1689 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 183 | X-RAY DIFFRACTION | f_plane_restr0.004 | 220 | X-RAY DIFFRACTION | f_dihedral_angle_d16.538 | 456 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.0016-2.2912 | 0.2395 | 154 | 0.1455 | 2775 | 2929 | 94 | 2.2912-2.8864 | 0.2206 | 161 | 0.1625 | 2839 | 3000 | 97 | 2.8864-34.9914 | 0.1799 | 164 | 0.1383 | 2933 | 3097 | 98 |
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Refinement TLS params. | Method: refined / Origin x: -6.1287 Å / Origin y: 5.8651 Å / Origin z: -9.9589 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0867 Å2 | 0.0019 Å2 | -0.005 Å2 | - | 0.0989 Å2 | -0.0125 Å2 | - | - | 0.0964 Å2 |
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L | 1.3659 °2 | -0.104 °2 | -0.3517 °2 | - | 1.4074 °2 | -0.1903 °2 | - | - | 2.7765 °2 |
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S | -0.0579 Å ° | -0.0378 Å ° | 0.0115 Å ° | 0.0533 Å ° | 0.0243 Å ° | -0.0358 Å ° | 0.0622 Å ° | 0.0006 Å ° | 0.0265 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 | allA2 - 156 | 2 | X-RAY DIFFRACTION | 1 | allB1 | 3 | X-RAY DIFFRACTION | 1 | allC1 | 4 | X-RAY DIFFRACTION | 1 | allS1 - 221 | | | | | | | | |
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