Software | Name | Version | Classification |
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Aimless | | data scalingREFMAC | 5.8.0352refinementPDB_EXTRACT | 3.27 | data extractionXDS | | data reductionPHASER | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3pk2 Resolution: 1.85→46.19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.776 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.121 / 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 | 0.2106 | 2463 | 5.2 % | RANDOM |
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Rwork | 0.1729 | - | - | - |
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obs | 0.1749 | 45009 | 96.55 % | - |
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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: 125.04 Å2 / Biso mean: 35.734 Å2 / Biso min: 18.28 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.25 Å2 | 0 Å2 | 1.3 Å2 |
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2- | - | 0.52 Å2 | -0 Å2 |
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3- | - | - | -1.07 Å2 |
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Refinement step | Cycle: final / Resolution: 1.85→46.19 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3674 | 0 | 184 | 181 | 4039 |
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Biso mean | - | - | 58.82 | 41.69 | - |
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Num. residues | - | - | - | - | 490 |
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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_d0.01 | 0.012 | 4020 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.016 | 3396 | X-RAY DIFFRACTION | r_angle_refined_deg2.056 | 1.749 | 5629 | X-RAY DIFFRACTION | r_angle_other_deg0.689 | 1.622 | 7839 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.44 | 5 | 490 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg7.299 | 5 | 17 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.886 | 10 | 525 | X-RAY DIFFRACTION | r_chiral_restr0.079 | 0.2 | 600 | X-RAY DIFFRACTION | r_gen_planes_refined0.01 | 0.02 | 4561 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 831 | | | | | | | | | | |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.284 | 153 | - |
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Rwork | 0.238 | 3099 | - |
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all | - | 3252 | - |
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obs | - | - | 90.56 % |
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