Software | Name | Version | Classification |
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SCALEPACK | | data scalingHKL-2000 | | data reductionPHASER | 2.5.6phasingPHENIX | 1.9_1692refinementPDB_EXTRACT | 3.15 | data extraction | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→68.89 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 18.9 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.203 | 1274 | 10 % |
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Rwork | 0.1687 | 11461 | - |
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obs | 0.1721 | 12735 | 99.18 % |
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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: 94.79 Å2 / Biso mean: 28.1668 Å2 / Biso min: 11.46 Å2 |
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Refinement step | Cycle: final / Resolution: 1.89→68.89 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 861 | 0 | 0 | 127 | 988 |
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Biso mean | - | - | - | 37.42 | - |
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Num. residues | - | - | - | - | 114 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 880 | X-RAY DIFFRACTION | f_angle_d0.967 | 1185 | X-RAY DIFFRACTION | f_chiral_restr0.047 | 122 | X-RAY DIFFRACTION | f_plane_restr0.004 | 154 | X-RAY DIFFRACTION | f_dihedral_angle_d12.821 | 313 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.89-1.9651 | 0.2056 | 130 | 0.1682 | 1176 | 1306 | 94 | 1.9651-2.0546 | 0.1963 | 138 | 0.1628 | 1234 | 1372 | 99 | 2.0546-2.1629 | 0.2387 | 140 | 0.1698 | 1265 | 1405 | 100 | 2.1629-2.2984 | 0.2134 | 140 | 0.1654 | 1261 | 1401 | 100 | 2.2984-2.4759 | 0.2135 | 141 | 0.1829 | 1266 | 1407 | 100 | 2.4759-2.725 | 0.2564 | 140 | 0.1846 | 1262 | 1402 | 100 | 2.725-3.1194 | 0.2463 | 144 | 0.1931 | 1289 | 1433 | 100 | 3.1194-3.93 | 0.1765 | 146 | 0.1672 | 1313 | 1459 | 100 | 3.93-68.9328 | 0.1688 | 155 | 0.149 | 1395 | 1550 | 100 |
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Refinement TLS params. | Method: refined / Origin x: -29.2134 Å / Origin y: 10.7299 Å / Origin z: 4.443 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1251 Å2 | -0.0006 Å2 | 0.0191 Å2 | - | 0.1482 Å2 | 0.026 Å2 | - | - | 0.1205 Å2 |
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L | 2.0139 °2 | -0.6631 °2 | -0.1559 °2 | - | 4.4696 °2 | 1.2971 °2 | - | - | 1.7168 °2 |
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S | 0.1071 Å ° | 0.1668 Å ° | 0.0199 Å ° | -0.0628 Å ° | -0.1528 Å ° | -0.0908 Å ° | 0.0238 Å ° | -0.1324 Å ° | 0.0306 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 | allA3 - 116 | 2 | X-RAY DIFFRACTION | 1 | allS1 - 128 | | | | |
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