Software | Name | Version | Classification |
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MLPHARE | | phasingCNS | 0.9 | refinementDENZO | | data reductionSCALEPACK | | data scaling | | | |
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Refinement | Method to determine structure: SIRAS Phasing / Resolution: 2.75→38.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 151607.03 / Isotropic thermal model: GROUP / 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 | 0.273 | 1851 | 9.5 % | random |
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Rwork | 0.222 | - | - | - |
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all | - | 20548 | - | - |
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obs | - | 19506 | 87.8 % | - |
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Solvent computation | Solvent model: flat model / Bsol: 28.24 Å2 / ksol: 0.315288 e/Å3 |
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Displacement parameters | Biso mean: 33.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 7.4 Å2 | 0 Å2 | 6.69 Å2 |
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2- | - | -0.01 Å2 | 0 Å2 |
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3- | - | - | -7.39 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.47 Å | 0.38 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.57 Å | 0.44 Å |
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Refinement step | Cycle: LAST / Resolution: 2.75→38.45 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5670 | 0 | 98 | 91 | 5859 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.008 | X-RAY DIFFRACTION | c_angle_deg1.3 | X-RAY DIFFRACTION | c_dihedral_angle_d21.7 | X-RAY DIFFRACTION | c_improper_angle_d0.89 | | | | |
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LS refinement shell | Resolution: 2.75→2.85 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.397 | 127 | 7.9 % |
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Rwork | 0.344 | 1484 | - |
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obs | - | - | 72.5 % |
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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 | A3P_XPLOR_PAR.TXTA3P_XPLOR_TOP.TXTX-RAY DIFFRACTION | 3 | LIGANDS1.PARRTL_XPLOR_TOP.TXTX-RAY DIFFRACTION | 4 | WATER.PARAMWATER.TOPX-RAY DIFFRACTION | 5 | CIS_PEPTIDE.PARAM | | | | | | | | | |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement |
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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_deg21.7 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.89 | | | | |
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