Software | Name | Version | Classification |
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CNS | 1.1 | refinementCrystalClear | (MSC/RIGAKU)data reductionSCALEPACK | | data scalingCNS | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WDP Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2526968.69 / 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 | 0.252 | 1513 | 4.9 % | RANDOM |
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Rwork | 0.206 | - | - | - |
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obs | 0.206 | 30579 | 97.1 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.5074 Å2 / ksol: 0.406937 e/Å3 |
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Displacement parameters | Biso mean: 11.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.23 Å2 | 0.08 Å2 | 0 Å2 |
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2- | - | 2.23 Å2 | 0 Å2 |
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3- | - | - | -4.46 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.31 Å | 0.24 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.22 Å | 0.15 Å |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.9 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3921 | 0 | 0 | 327 | 4248 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.006 | | X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.82 | | X-RAY DIFFRACTION | c_mcbond_it1.17 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.82 | 2 | X-RAY DIFFRACTION | c_scbond_it1.99 | 2 | X-RAY DIFFRACTION | c_scangle_it2.75 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.27 | 250 | 5.2 % |
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Rwork | 0.221 | 4578 | - |
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obs | - | - | 93.9 % |
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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 | water_rep.paramwater.topX-RAY DIFFRACTION | 3 | ion.paramion.top | | | | | |
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