Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingPHASES | | phasingCNS | 1 | refinement | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→48.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 285605.05 / 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 | 0.267 | 9809 | 10.1 % | RANDOM |
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Rwork | 0.212 | - | - | - |
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all | 0.212 | 98094 | - | - |
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obs | 0.212 | 98094 | 93.8 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.6958 Å2 / ksol: 0.325539 e/Å3 |
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Displacement parameters | Biso mean: 29.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.76 Å2 | -4.11 Å2 | 1.4 Å2 |
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2- | - | -1.89 Å2 | -0.66 Å2 |
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3- | - | - | -1.88 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.37 Å | 0.28 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.33 Å | 0.18 Å |
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Refinement step | Cycle: LAST / Resolution: 2.3→48.78 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 16652 | 0 | 0 | 609 | 17261 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.007 | X-RAY DIFFRACTION | c_angle_deg1.3 | X-RAY DIFFRACTION | c_dihedral_angle_d20.1 | X-RAY DIFFRACTION | c_improper_angle_d0.78 | | | | |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.327 | 1199 | 9.6 % |
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Rwork | 0.231 | 11277 | - |
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obs | - | - | 80.5 % |
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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_REP.TOP | | | |
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Refinement | *PLUS Highest resolution: 2.3 Å / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.212 |
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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_angle_deg1.237 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg20.1 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.78 | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.327 / Rfactor Rwork: 0.231 |
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