Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementPDB_EXTRACT | 3.24 | data extractionxia2 | | data reductionxia2 | | data scalingPHASER | | phasing | | | | | |
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Refinement | Resolution: 2→29.192 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 23.75
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2271 | 835 | 4.83 % |
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Rwork | 0.1832 | - | - |
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obs | 0.1854 | 17276 | 97.98 % |
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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: 114.11 Å2 / Biso mean: 32.9813 Å2 / Biso min: 10.87 Å2 |
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Refinement step | Cycle: final / Resolution: 2→29.192 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1928 | 0 | 0 | 160 | 2088 |
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Biso mean | - | - | - | 38.67 | - |
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Num. residues | - | - | - | - | 250 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 1970 | X-RAY DIFFRACTION | f_angle_d1.048 | 2674 | X-RAY DIFFRACTION | f_chiral_restr0.044 | 286 | X-RAY DIFFRACTION | f_plane_restr0.005 | 360 | X-RAY DIFFRACTION | f_dihedral_angle_d14.959 | 722 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2-2.1253 | 0.2686 | 127 | 0.1997 | 2641 | 2768 | 96 | 2.1253-2.2894 | 0.2492 | 153 | 0.1868 | 2628 | 2781 | 97 | 2.2894-2.5196 | 0.2422 | 132 | 0.1846 | 2728 | 2860 | 98 | 2.5196-2.8839 | 0.2448 | 149 | 0.1893 | 2718 | 2867 | 99 | 2.8839-3.6324 | 0.2271 | 122 | 0.186 | 2800 | 2922 | 99 | 3.6324-29.1947 | 0.2026 | 152 | 0.1744 | 2926 | 3078 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -5.8702 Å / Origin y: -18.4632 Å / Origin z: 23.9284 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0936 Å2 | -0.0002 Å2 | 0.0114 Å2 | - | 0.0936 Å2 | 0.0053 Å2 | - | - | 0.1198 Å2 |
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L | 0.8269 °2 | 0.0701 °2 | -0.1383 °2 | - | 0.8674 °2 | 0.0832 °2 | - | - | 1.7996 °2 |
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S | -0.0127 Å ° | 0.0267 Å ° | -0.031 Å ° | -0.0955 Å ° | 0.0197 Å ° | -0.0102 Å ° | -0.003 Å ° | 0.0192 Å ° | -0.0004 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 - 127 | 2 | X-RAY DIFFRACTION | 1 | allB3 - 127 | 3 | X-RAY DIFFRACTION | 1 | allS1 - 160 | | | | | | |
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