Software | Name | Version | Classification |
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GLRF | | phasingCNS | 1 | refinementDENZO | | data reductionSCALEPACK | | data scaling | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2999950.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.259 | 2471 | 7.5 % | RANDOM |
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Rwork | 0.226 | - | - | - |
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all | 0.226 | 32885 | - | - |
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obs | 0.226 | 32752 | 96.4 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.48 Å2 / ksol: 0.414 e/Å3 |
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Displacement parameters | Biso mean: 26.1 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -4.38 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -4.38 Å2 | 0 Å2 |
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3- | - | - | 8.77 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.28 Å | 0.24 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.11 Å | 0.07 Å |
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Refinement step | Cycle: LAST / Resolution: 2→19.72 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3341 | 0 | 0 | 183 | 3524 |
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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_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d21.9 | | X-RAY DIFFRACTION | c_improper_angle_d0.9 | | X-RAY DIFFRACTION | c_mcbond_it1.42 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.25 | 2 | X-RAY DIFFRACTION | c_scbond_it2.03 | 2 | X-RAY DIFFRACTION | c_scangle_it2.97 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.247 | 399 | 7.7 % |
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Rwork | 0.221 | 4785 | - |
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obs | - | 4785 | 93.7 % |
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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.TOP | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS σ(F): 1 / % reflection Rfree: 7.5 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 26.1 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_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg21.9 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.9 | | 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: 0.247 / % reflection Rfree: 7.7 % / Rfactor Rwork: 0.221 |
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