Software | Name | Version | Classification |
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ADSC | Quantumdata collectionEPMR | | phasingCNS | 1.3 | refinementHKL-2000 | | data reductionSCALEPACK | | data scalingPHENIX | 1.8.1_1168refinement | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.748 Å / SU ML: 0.36 / Isotropic thermal model: RESTRAINED / σ(F): 1.36 / Phase error: 24.94 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2559 | 1020 | 9.95 % |
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Rwork | 0.1823 | - | - |
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obs | 0.1895 | 10255 | 99.89 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 36.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.42 Å | 0.32 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.46 Å | 0.37 Å |
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Refinement step | Cycle: LAST / Resolution: 2.8→47.748 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2372 | 0 | 10 | 55 | 2437 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 2435 | X-RAY DIFFRACTION | f_angle_d1.315 | 3281 | X-RAY DIFFRACTION | f_dihedral_angle_d17.047 | 899 | X-RAY DIFFRACTION | f_chiral_restr0.097 | 349 | X-RAY DIFFRACTION | f_plane_restr0.005 | 423 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.8-2.9476 | 0.349 | 158 | 0.245 | 1304 | X-RAY DIFFRACTION | 100 | 2.9476-3.1322 | 0.2711 | 146 | 0.2023 | 1287 | X-RAY DIFFRACTION | 100 | 3.1322-3.374 | 0.2936 | 141 | 0.202 | 1299 | X-RAY DIFFRACTION | 100 | 3.374-3.7135 | 0.2545 | 138 | 0.1777 | 1316 | X-RAY DIFFRACTION | 100 | 3.7135-4.2505 | 0.2551 | 151 | 0.1594 | 1307 | X-RAY DIFFRACTION | 100 | 4.2505-5.3541 | 0.2015 | 133 | 0.1547 | 1353 | X-RAY DIFFRACTION | 100 | 5.3541-47.755 | 0.2372 | 153 | 0.1886 | 1369 | X-RAY DIFFRACTION | 99 |
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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 | dna-rna_rep.param | dna-rna.top | X-RAY DIFFRACTION | 3 | water_rep.paramwater.topX-RAY DIFFRACTION | 4 | ion.paramion.topX-RAY DIFFRACTION | 5 | carbohydrate.paramcarbohydrate.top | | | | | | | |
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