Software | Name | Version | Classification |
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CNS | 1.1 | refinementDENZO | | data reductionSCALEPACK | | data scalingCNS | | phasing | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 624331.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.23 | 298 | 6.2 % | RANDOM |
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Rwork | 0.219 | - | - | - |
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obs | 0.219 | 4787 | 89.5 % | - |
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all | - | 5347 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.222 Å2 / ksol: 0.35757 e/Å3 |
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Displacement parameters | Biso mean: 40.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.79 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -10.45 Å2 | 0 Å2 |
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3- | - | - | 9.66 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.38 Å | 0.35 Å |
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Luzzati d res low | - | 10 Å |
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Luzzati sigma a | 0.46 Å | 0.35 Å |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 978 | 15 | 48 | 1041 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.007 | X-RAY DIFFRACTION | c_angle_deg0.9 | X-RAY DIFFRACTION | c_dihedral_angle_d15 | X-RAY DIFFRACTION | c_improper_angle_d1.32 | | | | |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.346 | 43 | 6.9 % |
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Rwork | 0.325 | 579 | - |
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obs | - | - | 72.7 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMION.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAMDNA-RNA.TOP | X-RAY DIFFRACTION | 3 | DNA-RNA_REP.PARAM | ION.TOPX-RAY DIFFRACTION | 4 | ION.PARAMSPERMINE.TOPX-RAY DIFFRACTION | 5 | SPERMINE.PARAM | | | | | | | |
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