Software | Name | Version | Classification |
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PHENIX | 1.19.2_4158refinementXDS | | data scalingPHENIX | 1.19.2_4158phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XDH Resolution: 1.63→20.33 Å / SU ML: 0.2144 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.4293 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2466 | 1876 | 10.03 % |
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Rwork | 0.2248 | 16827 | - |
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obs | 0.2271 | 9706 | 91.83 % |
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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 mean: 47.64 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.63→20.33 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 680 | 9 | 41 | 730 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0082 | 766 | X-RAY DIFFRACTION | f_angle_d0.9509 | 1188 | X-RAY DIFFRACTION | f_chiral_restr0.0448 | 126 | X-RAY DIFFRACTION | f_plane_restr0.0059 | 32 | X-RAY DIFFRACTION | f_dihedral_angle_d34.6109 | 312 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.63-1.67 | 0.4331 | 151 | 0.3925 | 1311 | X-RAY DIFFRACTION | 92.3 | 1.67-1.72 | 0.4133 | 139 | 0.3402 | 1260 | X-RAY DIFFRACTION | 92.4 | 1.72-1.78 | 0.35 | 146 | 0.3627 | 1322 | X-RAY DIFFRACTION | 92.33 | 1.78-1.84 | 0.3873 | 153 | 0.3201 | 1307 | X-RAY DIFFRACTION | 92.17 | 1.84-1.92 | 0.2514 | 135 | 0.2883 | 1283 | X-RAY DIFFRACTION | 90.55 | 1.92-2 | 0.3284 | 138 | 0.2522 | 1307 | X-RAY DIFFRACTION | 92.87 | 2-2.11 | 0.3491 | 143 | 0.259 | 1278 | X-RAY DIFFRACTION | 93.12 | 2.11-2.24 | 0.278 | 148 | 0.2502 | 1316 | X-RAY DIFFRACTION | 92.08 | 2.24-2.41 | 0.3378 | 147 | 0.2606 | 1336 | X-RAY DIFFRACTION | 92.57 | 2.41-2.66 | 0.2692 | 139 | 0.2356 | 1273 | X-RAY DIFFRACTION | 91.33 | 2.66-3.04 | 0.2948 | 144 | 0.2881 | 1294 | X-RAY DIFFRACTION | 91.83 | 3.04-3.82 | 0.299 | 140 | 0.2151 | 1287 | X-RAY DIFFRACTION | 90.32 | 3.83-20.33 | 0.1485 | 153 | 0.1558 | 1253 | X-RAY DIFFRACTION | 90.13 |
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Refinement TLS params. | Method: refined / Origin x: 6.77914808831 Å / Origin y: 22.3619387789 Å / Origin z: 12.33412235 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.407971209573 Å2 | -0.032118575277 Å2 | -0.0345599869131 Å2 | - | 0.259381497884 Å2 | 0.0540977792313 Å2 | - | - | 0.235216733278 Å2 |
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L | 7.66078635288 °2 | -1.20759052384 °2 | -0.949955428536 °2 | - | 3.04593413123 °2 | -0.000220425744687 °2 | - | - | 2.7331353797 °2 |
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S | 0.247544869467 Å ° | -0.24367738702 Å ° | -0.182766793532 Å ° | 0.00782340361514 Å ° | -0.175398135313 Å ° | -0.0992429853606 Å ° | 0.103777021305 Å ° | -0.0257358215622 Å ° | -0.0328507014082 Å ° |
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Refinement TLS group | Selection details: all |
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