Software | Name | Version | Classification |
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CNS | | refinementMOSFLM | | data reduction CCP4 | (SCALA)data scalingCNS | | phasing | | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.75→23.33 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 157528.71 / Data cutoff low absF: 0 / Isotropic thermal model: ANISOTROPIC, RESTRAINED / 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 | 0.2867 | 261 | 5.4 % | RANDOM |
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Rwork | 0.2277 | - | - | - |
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all | 0.2311 | 4812 | - | - |
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obs | 0.2311 | 4812 | 91 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.17 Å2 / ksol: 0.326 e/Å3 |
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Displacement parameters | Biso mean: 81.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -5.3 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 45.44 Å2 | 0 Å2 |
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3- | - | - | -40.13 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.56 Å | 0.41 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.62 Å | 0.57 Å |
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Refinement step | Cycle: LAST / Resolution: 2.75→23.33 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 861 | 0 | 0 | 16 | 877 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.013 | | X-RAY DIFFRACTION | c_angle_deg1.5 | | X-RAY DIFFRACTION | c_dihedral_angle_d20.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.73 | | X-RAY DIFFRACTION | c_mcbond_it3.12 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it4.7 | 2 | X-RAY DIFFRACTION | c_scbond_it4.84 | 2 | X-RAY DIFFRACTION | c_scangle_it6.82 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.088 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.527 | 36 | 5.2 % |
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Rwork | 0.4 | 654 | - |
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obs | - | - | 80.4 % |
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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 Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5.4 % / Rfactor obs: 0.228 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 81.6 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_deg1.5 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg20.3 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.73 | | X-RAY DIFFRACTION | c_mcbond_it3.12 | 1.5 | X-RAY DIFFRACTION | c_scbond_it4.84 | 2 | X-RAY DIFFRACTION | c_mcangle_it4.7 | 2 | X-RAY DIFFRACTION | c_scangle_it6.82 | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.527 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.4 |
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