Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE)refinementXDS | | data reductionSCALA | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BNA Resolution: 1.32→25.322 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 19.25 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1823 | 1516 | 9.8 % |
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Rwork | 0.1385 | - | - |
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obs | 0.1426 | 15416 | 95.62 % |
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Solvent computation | Shrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.66 Å2 / ksol: 0.528 e/Å3 |
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Displacement parameters | Biso mean: 23.78 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.0359 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.5813 Å2 | 0 Å2 |
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3- | - | - | 0.4545 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.32→25.322 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 486 | 1 | 131 | 618 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.017 | 547 | X-RAY DIFFRACTION | f_angle_d2.087 | 839 | X-RAY DIFFRACTION | f_dihedral_angle_d30.264 | 232 | X-RAY DIFFRACTION | f_chiral_restr0.099 | 94 | X-RAY DIFFRACTION | f_plane_restr0.035 | 24 | | | | | |
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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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1.3201-1.3627 | 0.2526 | 126 | 0.1777 | 1127 | X-RAY DIFFRACTION | 88 | 1.3627-1.4114 | 0.2391 | 132 | 0.1614 | 1185 | X-RAY DIFFRACTION | 91 | 1.4114-1.4679 | 0.2079 | 128 | 0.1382 | 1225 | X-RAY DIFFRACTION | 93 | 1.4679-1.5347 | 0.1797 | 129 | 0.1344 | 1171 | X-RAY DIFFRACTION | 91 | 1.5347-1.6156 | 0.1832 | 136 | 0.1204 | 1258 | X-RAY DIFFRACTION | 97 | 1.6156-1.7168 | 0.1799 | 137 | 0.107 | 1266 | X-RAY DIFFRACTION | 97 | 1.7168-1.8493 | 0.1608 | 141 | 0.1083 | 1293 | X-RAY DIFFRACTION | 98 | 1.8493-2.0353 | 0.1787 | 142 | 0.1292 | 1299 | X-RAY DIFFRACTION | 98 | 2.0353-2.3296 | 0.2268 | 143 | 0.1415 | 1314 | X-RAY DIFFRACTION | 99 | 2.3296-2.9344 | 0.1948 | 147 | 0.1571 | 1343 | X-RAY DIFFRACTION | 99 | 2.9344-25.3264 | 0.1607 | 155 | 0.1406 | 1419 | X-RAY DIFFRACTION | 99 |
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