Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingCNS | 1.1 | refinementMOLREP | | phasing | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I4K Resolution: 1.68→35.28 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2411083.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.239 | 6658 | 5 % | RANDOM |
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Rwork | 0.217 | - | - | - |
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all | 0.228 | 132219 | - | - |
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obs | 0.228 | 132219 | 98.7 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.9717 Å2 / ksol: 0.374549 e/Å3 |
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Displacement parameters | Biso mean: 23.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.44 Å2 | 0 Å2 | -2.6 Å2 |
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2- | - | -2.18 Å2 | 0 Å2 |
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3- | - | - | -0.26 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.23 Å | 0.21 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.09 Å | 0.07 Å |
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Refinement step | Cycle: LAST / Resolution: 1.68→35.28 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 8302 | 0 | 0 | 474 | 8776 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.004 | | X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d24.1 | | X-RAY DIFFRACTION | c_improper_angle_d0.73 | | X-RAY DIFFRACTION | c_mcbond_it1.32 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.08 | 2 | X-RAY DIFFRACTION | c_scbond_it2.36 | 2 | X-RAY DIFFRACTION | c_scangle_it3.66 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.68→1.74 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.259 | 1058 | 4.9 % |
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Rwork | 0.242 | 20547 | - |
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obs | - | 20547 | 97.4 % |
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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 | WATER_REP.PARAMWATER.TOP | | | |
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