Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingMLPHARE | | phasingCNS | 1 | refinement | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→13 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 466472.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.266 | 518 | 9.8 % | RANDOM |
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Rwork | 0.237 | - | - | - |
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obs | 0.237 | 5310 | 94.6 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.74 Å2 / ksol: 0.313 e/Å3 |
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Displacement parameters | Biso mean: 41.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.59 Å2 | -13.62 Å2 | 0 Å2 |
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2- | - | -2.59 Å2 | 0 Å2 |
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3- | - | - | 5.18 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.44 Å | 0.34 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.41 Å | 0.33 Å |
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Refinement step | Cycle: LAST / Resolution: 2.1→13 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 486 | 0 | 100 | 586 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.018 | X-RAY DIFFRACTION | c_angle_deg2.1 | X-RAY DIFFRACTION | c_dihedral_angle_d17.1 | X-RAY DIFFRACTION | c_improper_angle_d1.88 | | | | |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.362 | 84 | 10.5 % |
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Rwork | 0.318 | 717 | - |
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obs | - | - | 88 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | DNA-RNA_REP.PARAM | DNA-RNA.TOP | X-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER.TOP | | | |
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Refinement | *PLUS Highest resolution: 2.1 Å / % reflection Rfree: 10 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.002 | X-RAY DIFFRACTION | c_angle_deg2.07 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg0.171 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.88 | | | | | | |
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