Software | Name | Version | Classification |
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CNS | 1.1 | refinementDNA | | data collectionDENZO | | data reductionSCALEPACK | | data scalingSHARP | | phasing | | | | |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→18.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 868917.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.227 | 3583 | 7.8 % | RANDOM |
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Rwork | 0.221 | - | - | - |
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obs | 0.221 | 45890 | 98.6 % | - |
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all | - | 46527 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1428 Å2 / ksol: 0.383433 e/Å3 |
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Displacement parameters | Biso mean: 31.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.57 Å2 | 0 Å2 | -0.47 Å2 |
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2- | - | 13.44 Å2 | 0 Å2 |
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3- | - | - | -10.86 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.23 Å | 0.23 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.33 Å | 0.31 Å |
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Refinement step | Cycle: LAST / Resolution: 1.5→18.44 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 980 | 62 | 164 | 1206 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.006 | X-RAY DIFFRACTION | c_angle_deg1.4 | X-RAY DIFFRACTION | c_dihedral_angle_d10.1 | X-RAY DIFFRACTION | c_improper_angle_d4.9 | | | | |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.413 | 636 | 8.3 % |
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Rwork | 0.413 | 7071 | - |
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obs | - | - | 99 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | water_rep.paramwater.topX-RAY DIFFRACTION | 2 | luc.paramdna-rna.top | X-RAY DIFFRACTION | 3 | ion.paramion.topX-RAY DIFFRACTION | 4 | ums_xplor.paramums_xplor.topX-RAY DIFFRACTION | 5 | ribostamycine.paramribostamycine.top | | | | | | | | |
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