Software | Name | Version | Classification |
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CNS | 1.1 | refinementMOSFLM | | data reduction CCP4 | (SCALA)data scalingBEAST | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2344125.44 / Data cutoff high rms absF: 2344125.44 / 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 | 0.229 | 1716 | 4.9 % | RANDOM |
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Rwork | 0.215 | - | - | - |
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all | 0.216 | 35062 | - | - |
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obs | 0.215 | 34733 | 98.9 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.751 Å2 / ksol: 0.342248 e/Å3 |
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Displacement parameters | Biso mean: 58.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.37 Å | 0.35 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.41 Å | 0.34 Å |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.63 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2698 | 0 | 96 | 166 | 2960 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.008 | | X-RAY DIFFRACTION | c_angle_deg1.1 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.6 | | X-RAY DIFFRACTION | c_improper_angle_d0.87 | | X-RAY DIFFRACTION | c_mcbond_it1.36 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.37 | 2 | X-RAY DIFFRACTION | c_scbond_it1.95 | 2 | X-RAY DIFFRACTION | c_scangle_it3.1 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.326 | 261 | 4.8 % |
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Rwork | 0.34 | 5144 | - |
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obs | - | - | 94.7 % |
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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 | NADPH.PARAMNADPH.TOP | | | | | |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 19.7 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.217 |
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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_angle_deg1.15 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg23.6 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.87 | | | | | |
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