Software | Name | Version | Classification |
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CNS | 1.1 | refinementBOS | | data collectiond*TREK | | data scalingCNS | | phasing | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→49.32 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 441185.1 / 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 | 0.289 | 999 | 7.4 % | RANDOM |
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Rwork | 0.266 | - | - | - |
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all | 0.266 | 13511 | - | - |
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obs | 0.266 | 13415 | 99.3 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.880832 e/Å3 |
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Displacement parameters | Biso mean: 69.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 11.87 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 11.87 Å2 | 0 Å2 |
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3- | - | - | -23.74 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.48 Å | 0.39 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.35 Å | 0.39 Å |
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Refinement step | Cycle: LAST / Resolution: 2.9→49.32 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 2029 | 57 | 88 | 2174 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.01 | | X-RAY DIFFRACTION | c_angle_deg1.6 | | X-RAY DIFFRACTION | c_dihedral_angle_d17.3 | | X-RAY DIFFRACTION | c_improper_angle_d2.31 | | X-RAY DIFFRACTION | c_mcbond_it1.38 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.56 | 2 | X-RAY DIFFRACTION | c_scbond_it1.63 | 2 | X-RAY DIFFRACTION | c_scangle_it2.61 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.416 | 162 | 7.3 % |
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Rwork | 0.427 | 2056 | - |
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obs | - | - | 98.9 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | dna-rna_rep.param | dna-rna_rep.top | X-RAY DIFFRACTION | 2 | ion2.paramion2.topX-RAY DIFFRACTION | 3 | sam3.paramsam3.topX-RAY DIFFRACTION | 4 | water_rep.paramwater_rep.top | | | | | |
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