Software | Name | Version | Classification |
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CNS | 1.1 | refinementDENZO | | data reductionSCALEPACK | | data scalingSnB | | phasingSOLVE | | phasing | | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2974439.24 / Data cutoff high rms absF: 2974439.24 / 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 | 0.296 | 1138 | 5.2 % | RANDOM |
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Rwork | 0.248 | - | - | - |
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all | 0.248 | - | - | - |
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obs | 0.248 | 21804 | 92.9 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.251692 e/Å3 |
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Displacement parameters | Biso mean: 55.8 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -19.33 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -9.08 Å2 | 0 Å2 |
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3- | - | - | 28.41 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.52 Å | 0.44 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.99 Å | 0.95 Å |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4176 | 0 | 81 | 85 | 4342 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.012 | X-RAY DIFFRACTION | c_angle_deg1.7 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_improper_angle_d1.27 | | | | |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.449 | 168 | 5.3 % |
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Rwork | 0.429 | 3019 | - |
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obs | - | 3187 | 83 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1X-RAY DIFFRACTION | 2 | ION.PARAM&_1_TOPOLOGY_INFILE_2X-RAY DIFFRACTION | 3 | SAM.PAR&_1_TOPOLOGY_INFILE_3X-RAY DIFFRACTION | 4 | WATER_REP.PARAM&_1_TOPOLOGY_INFILE_4X-RAY DIFFRACTION | 5 | SO4.PAR&_1_TOPOLOGY_INFILE_5 | | | | | | | | | |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 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_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.27 | | |
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