Software | Name | Version | Classification |
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SCALA | | data scalingSOLVE | | phasing CCP4 | | model buildingCNS | 1 | refinement CCP4 | (SCALA)data scaling CCP4 | | phasing | | | | | | |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→29.45 Å / Rfactor Rfree error: 0.01 / 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 | 0.234 | 588 | 5.1 % | RANDOM |
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Rwork | 0.194 | - | - | - |
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all | 0.198 | 11582 | - | - |
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obs | - | 11582 | 99 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.2048 Å2 / ksol: 0.341422 e/Å3 |
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Displacement parameters | Biso mean: 17.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.78 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 2.16 Å2 | 0 Å2 |
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3- | - | - | -0.38 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.31 Å | 0.25 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.3 Å | 0.2 Å |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.45 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1814 | 0 | 0 | 102 | 1916 |
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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_d21.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.84 | | X-RAY DIFFRACTION | c_mcbond_it1.2 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.86 | 2 | X-RAY DIFFRACTION | c_scbond_it2.25 | 2 | X-RAY DIFFRACTION | c_scangle_it3.38 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.311 | 87 | 4.7 % |
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Rwork | 0.222 | 1779 | - |
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obs | - | - | 98.8 % |
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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.PARAM | | | |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.229 |
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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_deg1.3 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg21.3 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.84 | | | | | |
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