Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingAMoRE | | phasingCNS | 0.4 | refinement | | | |
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Refinement | Resolution: 1.8→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 381569.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.218 | 1953 | 5 % | RANDOM |
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Rwork | 0.199 | - | - | - |
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all | 0.218 | 43228 | - | - |
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obs | 0.197 | 38784 | 87.7 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.77 Å2 / ksol: 0.33 e/Å3 |
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Displacement parameters | Biso mean: 34.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.24 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.09 Å2 | 0 Å2 |
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3- | - | - | 0.16 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.24 Å | 0.21 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.19 Å | 0.17 Å |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4160 | 0 | 2 | 603 | 4765 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.005 | | X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.5 | | X-RAY DIFFRACTION | c_improper_angle_d0.72 | | X-RAY DIFFRACTION | c_mcbond_it3.03 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it4.6 | 2 | X-RAY DIFFRACTION | c_scbond_it4.25 | 2 | X-RAY DIFFRACTION | c_scangle_it6.38 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.253 | 241 | 5.5 % |
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Rwork | 0.235 | 4151 | - |
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obs | - | - | 60.7 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PAPROTEIN.TOPX-RAY DIFFRACTION | 2 | ION.PARAMION.TOPX-RAY DIFFRACTION | 3 | WATER_REP.PARAWATER_REP.TOP | | | | | |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 34.4 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg23.5 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.72 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.253 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.235 |
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