Software | Name | Version | Classification |
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REFMAC | 5.8.0189refinementxia2 | | data scalingPDB_EXTRACT | 3.25 | data extractionxia2 | | data reductionPHASER | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→43.02 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.779 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / 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 | 0.1286 | 7817 | 5 % | RANDOM |
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Rwork | 0.1111 | - | - | - |
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obs | 0.112 | 148310 | 93.11 % | - |
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: MASK |
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Displacement parameters | Biso max: 70.19 Å2 / Biso mean: 17.774 Å2 / Biso min: 9.34 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.07 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.07 Å2 | 0 Å2 |
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3- | - | - | 0.13 Å2 |
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Refinement step | Cycle: final / Resolution: 1.18→43.02 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3142 | 0 | 5 | 661 | 3808 |
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Biso mean | - | - | 31.39 | 32.44 | - |
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Num. residues | - | - | - | - | 424 |
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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_d0.012 | 0.019 | 3501 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 3258 | X-RAY DIFFRACTION | r_angle_refined_deg1.595 | 1.971 | 4822 | X-RAY DIFFRACTION | r_angle_other_deg1.013 | 3 | 7595 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.839 | 5 | 506 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg31.239 | 23.467 | 150 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.929 | 15 | 570 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg21.514 | 15 | 27 | X-RAY DIFFRACTION | r_chiral_restr0.114 | 0.2 | 536 | X-RAY DIFFRACTION | r_gen_planes_refined0.01 | 0.021 | 4080 | X-RAY DIFFRACTION | r_gen_planes_other0.002 | 0.02 | 726 | X-RAY DIFFRACTION | r_rigid_bond_restr1.865 | 3 | 6759 | X-RAY DIFFRACTION | r_sphericity_free22.266 | 5 | 432 | X-RAY DIFFRACTION | r_sphericity_bonded6.993 | 5 | 6876 | | | | | | | | | | | | | | |
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LS refinement shell | Resolution: 1.18→1.211 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.275 | 380 | - |
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Rwork | 0.256 | 7167 | - |
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all | - | 7547 | - |
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obs | - | - | 61.65 % |
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