Software | Name | Version | Classification |
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HKL-2000 | | data collectionMOLREP | | phasingCNS | 1.1 | refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ESC Resolution: 1.75→37.1 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1591373 / 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 | 0.223 | 1256 | 4.8 % | RANDOM |
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Rwork | 0.186 | - | - | - |
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obs | 0.186 | 25973 | 99.7 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.3638 Å2 / ksol: 0.386993 e/Å3 |
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Displacement parameters | Biso mean: 18.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.84 Å2 | 1.13 Å2 | 0 Å2 |
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2- | - | 1.84 Å2 | 0 Å2 |
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3- | - | - | -3.67 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.21 Å | 0.18 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.12 Å | 0.1 Å |
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Refinement step | Cycle: LAST / Resolution: 1.75→37.1 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1700 | 0 | 16 | 218 | 1934 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.009 | | X-RAY DIFFRACTION | c_angle_deg1.5 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.1 | | X-RAY DIFFRACTION | c_improper_angle_d0.89 | | X-RAY DIFFRACTION | c_mcbond_it1.22 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.85 | 2 | X-RAY DIFFRACTION | c_scbond_it2.07 | 2 | X-RAY DIFFRACTION | c_scangle_it2.95 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.248 | 197 | 4.8 % |
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Rwork | 0.21 | 3904 | - |
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obs | - | - | 95.3 % |
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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.param1PE.topX-RAY DIFFRACTION | 3 | 1PE.param | | | | | |
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