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: 1.65→46.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.575 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 / 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 | 0.2007 | 3822 | 5.2 % | RANDOM |
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Rwork | 0.1689 | - | - | - |
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obs | 0.1706 | 69370 | 99.83 % | - |
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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: 90.91 Å2 / Biso mean: 18.693 Å2 / Biso min: 8.37 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.14 Å2 | 0 Å2 | 0.04 Å2 |
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2- | - | -0.07 Å2 | -0 Å2 |
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3- | - | - | -0.08 Å2 |
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Refinement step | Cycle: final / Resolution: 1.65→46.01 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3669 | 0 | 184 | 454 | 4307 |
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Biso mean | - | - | 33.87 | 32.86 | - |
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Num. residues | - | - | - | - | 491 |
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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 | 0.012 | 4064 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.016 | 3256 | X-RAY DIFFRACTION | r_angle_refined_deg3.236 | 1.744 | 5707 | X-RAY DIFFRACTION | r_angle_other_deg0.567 | 1.552 | 7549 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.437 | 5 | 505 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg13.671 | 10 | 16 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.634 | 10 | 520 | X-RAY DIFFRACTION | r_chiral_restr0.083 | 0.2 | 608 | X-RAY DIFFRACTION | r_gen_planes_refined0.011 | 0.02 | 4694 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 842 | | | | | | | | | | |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.277 | 266 | - |
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Rwork | 0.236 | 5076 | - |
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all | - | 5342 | - |
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obs | - | - | 99.55 % |
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