Software | Name | Version | Classification |
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CNS | 1.1 | refinementHKL-2000 | | data collectionHKL-2000 | | data reductionHKL-2000 | | data scalingMOLREP | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1E19 Resolution: 1.8→37.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2070175.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.225 | 2956 | 5 % | RANDOM |
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Rwork | 0.2 | - | - | - |
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obs | 0.2 | 58985 | 99.8 % | - |
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all | - | 58985 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.9369 Å2 / ksol: 0.330158 e/Å3 |
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Displacement parameters | Biso mean: 27.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.68 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -3.01 Å2 | 0 Å2 |
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3- | - | - | 2.33 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.24 Å | 0.2 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.15 Å | 0.13 Å |
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Refinement step | Cycle: LAST / Resolution: 1.8→37.48 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4698 | 0 | 0 | 622 | 5320 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.007 | | X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.6 | | X-RAY DIFFRACTION | c_improper_angle_d0.88 | | X-RAY DIFFRACTION | c_mcbond_it1.31 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.06 | 2 | X-RAY DIFFRACTION | c_scbond_it2 | 2 | X-RAY DIFFRACTION | c_scangle_it2.99 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.259 | 441 | 4.6 % |
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Rwork | 0.232 | 9202 | - |
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obs | - | - | 99.8 % |
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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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