Software | Name | Version | Classification |
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PHENIX | | refinementAimless | 0.5.27data scalingPHASER | 2.7.16phasingPDB_EXTRACT | 3.24 | data extractionDIALS | | data reduction | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+81 / Resolution: 2.901→38.346 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 25.67
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2931 | 293 | 9.98 % |
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Rwork | 0.2345 | - | - |
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obs | 0.2401 | 2937 | 99.73 % |
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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: 382.08 Å2 / Biso mean: 130.8393 Å2 / Biso min: 45.83 Å2 |
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Refinement step | Cycle: final / Resolution: 2.901→38.346 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 785 | 23 | 0 | 808 |
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Biso mean | - | - | 72.19 | - | - |
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Num. residues | - | - | - | - | 36 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 905 | X-RAY DIFFRACTION | f_angle_d1.451 | 1410 | X-RAY DIFFRACTION | f_chiral_restr0.063 | 180 | X-RAY DIFFRACTION | f_plane_restr0.009 | 38 | X-RAY DIFFRACTION | f_dihedral_angle_d20.792 | 431 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 % Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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2.9011-3.6547 | 0.3639 | 144 | 0.2948 | 1303 | 1447 | 3.6547-38.3495 | 0.2712 | 149 | 0.2148 | 1341 | 1490 |
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Refinement TLS params. | Method: refined / Origin x: 1.8221 Å / Origin y: 23.97 Å / Origin z: 7.1348 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2342 Å2 | -0.6335 Å2 | 0.0008 Å2 | - | 1.7129 Å2 | -0.3018 Å2 | - | - | 0.6205 Å2 |
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L | 0.2038 °2 | -0.0707 °2 | 0.0898 °2 | - | 0.0275 °2 | -0.0138 °2 | - | - | 0.3009 °2 |
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S | 0.2034 Å ° | -0.4164 Å ° | -0.1207 Å ° | 0.0366 Å ° | -0.0958 Å ° | -0.0795 Å ° | 0.5816 Å ° | -1.5486 Å ° | 0.1333 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 - 36 | 2 | X-RAY DIFFRACTION | 1 | allD1 | 3 | X-RAY DIFFRACTION | 1 | allC1 | | | | | | |
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