Software | Name | Version | Classification |
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XDS | | data reductionAMoRE | | phasingCNS | 0.9 | refinementXDS | | data scaling | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NKS Resolution: 2.5→33.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 961139.64 / 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 | 0.253 | 3917 | 10 % | RANDOM |
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Rwork | 0.22 | - | - | - |
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all | 0.2201 | 39038 | - | - |
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obs | 0.2201 | 39001 | 84.2 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.0305 Å2 / ksol: 0.33593 e/Å3 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.36 Å | 0.31 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.35 Å | 0.32 Å |
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Refinement step | Cycle: LAST / Resolution: 2.5→33.42 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4419 | 0 | 46 | 179 | 4644 |
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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_d21.8 | | X-RAY DIFFRACTION | c_improper_angle_d0.77 | | X-RAY DIFFRACTION | c_mcbond_it1.22 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.21 | 2 | X-RAY DIFFRACTION | c_scbond_it1.42 | 2 | X-RAY DIFFRACTION | c_scangle_it2.24 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.309 | 665 | 10.1 % |
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Rwork | 0.289 | 5915 | - |
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obs | - | - | 86.3 % |
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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.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | ADENOSINE.PARAMAMP.TOPOLOGY | | | | | |
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Refinement | *PLUS Highest resolution: 2.5 Å / Rfactor Rwork: 0.22 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg21.8 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.77 | | | | |
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