Software | Name | Version | Classification |
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CNS | 1 | refinementDENZO | | data reductionSCALEPACK | | data scaling | | |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→23.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3664358.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.235 | 1892 | 5 % | RANDOM |
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Rwork | 0.205 | - | - | - |
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obs | 0.222 | 37468 | 97.6 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.3718 Å2 / ksol: 0.406625 e/Å3 |
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Displacement parameters | Biso mean: 25.8 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 | 0.25 Å | 0.21 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.2 Å | 0.14 Å |
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Refinement step | Cycle: LAST / Resolution: 1.8→23.96 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2472 | 0 | 59 | 322 | 2853 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.006 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.4 | | X-RAY DIFFRACTION | c_improper_angle_d0.79 | | X-RAY DIFFRACTION | c_mcbond_it1.08 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.77 | 2 | X-RAY DIFFRACTION | c_scbond_it1.69 | 2 | X-RAY DIFFRACTION | c_scangle_it2.58 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.327 | 294 | 5.3 % |
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Rwork | 0.275 | 5236 | - |
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obs | - | - | 86.9 % |
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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-topology | X-RAY DIFFRACTION | 3 | dpc.pardpc.topX-RAY DIFFRACTION | 4 | ion.paramion.top | | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 25.8 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg22.4 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.79 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.327 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.275 |
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