Software | Name | Version | Classification |
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PHASES | | phasing X-PLOR | 3.851 | refinement | |
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Refinement | Resolution: 1.4→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.231 | 1520 | 9.8 % | RANDOM |
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Rwork | 0.188 | - | - | - |
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obs | 0.188 | 15483 | 79.8 % | - |
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all | - | 15558 | - | - |
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Displacement parameters | Biso mean: 13.1 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.18 Å | 0.15 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.1 Å | 0.13 Å |
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 958 | 0 | 0 | 127 | 1085 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | x_bond_d0.008 | | X-RAY DIFFRACTION | x_angle_deg1.2 | | X-RAY DIFFRACTION | x_dihedral_angle_d21.6 | | X-RAY DIFFRACTION | x_improper_angle_d0.71 | | X-RAY DIFFRACTION | x_mcbond_it0.94 | 1.5 | X-RAY DIFFRACTION | x_mcangle_it1.31 | 2 | X-RAY DIFFRACTION | x_scbond_it2.04 | 2 | X-RAY DIFFRACTION | x_scangle_it3.13 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.244 | 186 | 9.8 % |
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Rwork | 0.239 | 1711 | - |
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obs | - | - | 59.1 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMTOPHCSDX.PROX-RAY DIFFRACTION | 2 | | TOPH19.SOL | | |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 9.8 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 13.1 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | x_angle_deg1.2 | | X-RAY DIFFRACTION | x_dihedral_angle_d | | X-RAY DIFFRACTION | x_dihedral_angle_deg21.6 | | X-RAY DIFFRACTION | x_improper_angle_d | | X-RAY DIFFRACTION | x_improper_angle_deg0.71 | | X-RAY DIFFRACTION | x_mcbond_it0.94 | 1.5 | X-RAY DIFFRACTION | x_scbond_it2.04 | 2 | X-RAY DIFFRACTION | x_mcangle_it1.31 | 2 | X-RAY DIFFRACTION | x_scangle_it3.13 | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.244 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.239 |
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