Software | Name | Version | Classification |
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REFMAC | 5.8.0253refinementHKL-2000 | | data scalingPDB_EXTRACT | 3.25 | data extractionHKL-2000 | | data reductionPHENIX | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→28.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.204 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2033 | 3393 | 5 % | RANDOM |
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Rwork | 0.1707 | - | - | - |
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obs | 0.1723 | 64319 | 95.07 % | - |
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK |
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Displacement parameters | Biso max: 95.4 Å2 / Biso mean: 23.593 Å2 / Biso min: 14.46 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.12 Å2 | 0.06 Å2 | 0 Å2 |
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2- | - | 0.12 Å2 | -0 Å2 |
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3- | - | - | -0.38 Å2 |
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Refinement step | Cycle: final / Resolution: 1.9→28.5 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4793 | 0 | 23 | 305 | 5121 |
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Biso mean | - | - | 34.3 | 27.32 | - |
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Num. residues | - | - | - | - | 586 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target | Number |
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X-RAY DIFFRACTION | r_bond_refined_d0.013 | 0.013 | 4969 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.017 | 4319 | X-RAY DIFFRACTION | r_angle_refined_deg1.837 | 1.644 | 6759 | X-RAY DIFFRACTION | r_angle_other_deg1.474 | 1.575 | 10066 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.179 | 5 | 593 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.798 | 23.344 | 299 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.321 | 15 | 778 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.523 | 15 | 27 | X-RAY DIFFRACTION | r_chiral_restr0.09 | 0.2 | 614 | X-RAY DIFFRACTION | r_gen_planes_refined0.012 | 0.02 | 5628 | X-RAY DIFFRACTION | r_gen_planes_other0.003 | 0.02 | 1065 | | | | | | | | | | | |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.261 | 240 | - |
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Rwork | 0.199 | 4751 | - |
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all | - | 4991 | - |
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obs | - | - | 95.39 % |
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