Software | Name | Version | Classification |
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CNS | 1.1 | refinementDENZO | | data reductionSCALEPACK | | data scalingMLPHARE | | phasing | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→40.43 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1877215.28 / Data cutoff low absF: 0 / 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 | 0.252 | 3472 | 5.1 % | RANDOM |
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Rwork | 0.211 | - | - | - |
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all | 0.211 | 68519 | - | - |
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obs | 0.211 | 68519 | 97.4 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.4268 Å2 / ksol: 0.353232 e/Å3 |
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Displacement parameters | Biso mean: 34.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 15.09 Å2 | 0 Å2 | -0.82 Å2 |
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2- | - | -7.02 Å2 | 0 Å2 |
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3- | - | - | -8.07 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.33 Å | 0.27 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.32 Å | 0.27 Å |
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Refinement step | Cycle: LAST / Resolution: 2.3→40.43 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 9342 | 0 | 69 | 932 | 10343 |
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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_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.2 | | X-RAY DIFFRACTION | c_improper_angle_d1 | | X-RAY DIFFRACTION | c_mcbond_it0.3 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it0.57 | 2 | X-RAY DIFFRACTION | c_scbond_it0.25 | 2 | X-RAY DIFFRACTION | c_scangle_it0.44 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.304 | 577 | 5.3 % |
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Rwork | 0.265 | 10260 | - |
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obs | - | - | 93.4 % |
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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 | ION.PARAMWATER-TOPOLOGY | X-RAY DIFFRACTION | 3 | WATER_REP.PARAMION.TOP | | | | |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40.4 Å / % reflection Rfree: 5 % |
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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_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg22.2 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1 | | | | |
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.303 |
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