Software | Name | Version | Classification |
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CNS | 1.1 | refinementHKL-2000 | | data reductionSCALEPACK | | data scalingSHARP | | phasing | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.38→40.41 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1281589.91 / 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 | 0.262 | 492 | 5.1 % | RANDOM |
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Rwork | 0.231 | - | - | - |
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obs | 0.231 | 9725 | 91 % | - |
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all | - | 9725 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.91 Å2 / ksol: 0.38289 e/Å3 |
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Displacement parameters | Biso mean: 23.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.17 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.17 Å2 | 0 Å2 |
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3- | - | - | -0.34 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.34 Å | 0.31 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.42 Å | 0.24 Å |
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Refinement step | Cycle: LAST / Resolution: 2.38→40.41 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1554 | 0 | 3 | 54 | 1611 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.008 | X-RAY DIFFRACTION | c_angle_deg1.5 | X-RAY DIFFRACTION | c_dihedral_angle_d25.3 | X-RAY DIFFRACTION | c_improper_angle_d0.86 | | | | |
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LS refinement shell | Resolution: 2.38→2.53 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.351 | 30 | 3.7 % |
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Rwork | 0.329 | 780 | - |
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obs | - | - | 47.3 % |
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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 | IYR2.paramprotein_IYR2.topX-RAY DIFFRACTION | 3 | water_rep.paramIYR2.topX-RAY DIFFRACTION | 4 | ion.param | | | | | | | |
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