Software | Name | Version | Classification |
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CNS | 1.1 | refinementHKL-2000 | | data reductionSCALEPACK | | data scalingCNS | | phasing | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 618415.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.262 | 1323 | 9.8 % | RANDOM |
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Rwork | 0.243 | - | - | - |
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obs | 0.243 | 13509 | 97.9 % | - |
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all | - | 13794 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.0914 Å2 / ksol: 0.344799 e/Å3 |
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Displacement parameters | Biso mean: 44.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.92 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -16.51 Å2 | 0 Å2 |
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3- | - | - | 15.6 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.41 Å | 0.39 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.52 Å | 0.53 Å |
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 980 | 5 | 113 | 1098 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.006 | X-RAY DIFFRACTION | c_angle_deg1 | X-RAY DIFFRACTION | c_dihedral_angle_d8 | X-RAY DIFFRACTION | c_improper_angle_d1.49 | | | | |
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LS refinement shell | Resolution: 2.25→2.35 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.383 | 155 | 9.9 % |
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Rwork | 0.426 | 1404 | - |
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obs | - | - | 93.2 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 2 | LUC.PARAMDNA-RNA.TOP | X-RAY DIFFRACTION | 3 | ION.PARAMION2.TOPX-RAY DIFFRACTION | 4 | BRU_REP.PARAM | | | | | | |
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