Software | Name | Version | Classification |
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CNS | 1.1 | refinementCrystalClear | | data collectionCrystalClear | | data reductionCrystalClear | | data scalingAMoRE | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VE1 Resolution: 1.9→43.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1706618.66 / 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 | 0.214 | 3961 | 10.1 % | RANDOM |
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Rwork | 0.187 | - | - | - |
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obs | 0.187 | 39346 | 98 % | - |
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all | - | 40094 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.9472 Å2 / ksol: 0.37673 e/Å3 |
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Displacement parameters | Biso mean: 21.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.46 Å2 | 0.83 Å2 | 0 Å2 |
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2- | - | 0.46 Å2 | 0 Å2 |
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3- | - | - | -0.92 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.23 Å | 0.2 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.17 Å | 0.14 Å |
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Refinement step | Cycle: LAST / Resolution: 1.9→43.76 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2292 | 0 | 23 | 301 | 2616 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.005 | | X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.6 | | X-RAY DIFFRACTION | c_improper_angle_d0.76 | | X-RAY DIFFRACTION | c_mcbond_it1.17 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.75 | 2 | X-RAY DIFFRACTION | c_scbond_it21.66 | 2 | X-RAY DIFFRACTION | c_scangle_it12.11 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.273 | 629 | 10.5 % |
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Rwork | 0.244 | 5375 | - |
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obs | - | - | 91 % |
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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.paramwat.topX-RAY DIFFRACTION | 3 | 4mv.param4mv.topX-RAY DIFFRACTION | 4 | plp.paramplp.topX-RAY DIFFRACTION | 5 | etc.paramintshiff.top | | | | | | | | | |
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