Software | Name | Version | Classification |
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CNS | 1.1 | refinementHKL-2000 | | data reductionSCALEPACK | | data scalingCNS | | phasing | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RAM Resolution: 1.6→14.37 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1003948.67 / 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 | 0.218 | 612 | 9.7 % | RANDOM |
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Rwork | 0.207 | - | - | - |
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obs | 0.207 | 6341 | 98.5 % | - |
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all | - | 6341 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4827 Å2 / ksol: 0.380301 e/Å3 |
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Displacement parameters | Biso mean: 24.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.59 Å2 | -0.07 Å2 | 0 Å2 |
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2- | - | 1.59 Å2 | 0 Å2 |
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3- | - | - | -3.19 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.22 Å | 0.2 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.09 Å | 0.09 Å |
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Refinement step | Cycle: LAST / Resolution: 1.6→14.37 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 344 | 6 | 107 | 457 |
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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_d20.4 | X-RAY DIFFRACTION | c_improper_angle_d1.75 | | | | |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.359 | 87 | 9 % |
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Rwork | 0.333 | 880 | - |
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obs | - | - | 91.9 % |
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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 | DNA-RNA_REP.PARAM | DNA-RNA.TOP | X-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | ION.PARAMION.TOP | | | | | |
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 6340 / % reflection Rfree: 10 % / Rfactor Rfree: 0.215 |
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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_d0.0076 | X-RAY DIFFRACTION | c_angle_deg1.54 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg20.4 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.75 | | | | | | |
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