Software | Name | Version | Classification |
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Aimless | 0.7.4data scalingREFMAC | 5.8.0258refinementPDB_EXTRACT | 3.27 | data extractionAimless | | data reductionMOLREP | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3nqx Resolution: 2→20.13 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.583 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2878 | 1111 | 5.3 % | RANDOM |
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Rwork | 0.2376 | - | - | - |
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obs | 0.2401 | 19952 | 94.57 % | - |
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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: 55.96 Å2 / Biso mean: 21.632 Å2 / Biso min: 9.17 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.63 Å2 | -0 Å2 | 0 Å2 |
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2- | - | 3.22 Å2 | -0 Å2 |
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3- | - | - | -0.59 Å2 |
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Refinement step | Cycle: final / Resolution: 2→20.13 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2275 | 0 | 7 | 159 | 2441 |
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Biso mean | - | - | 28.01 | 28.43 | - |
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Num. residues | - | - | - | - | 299 |
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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_d0.009 | 0.013 | 2339 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.018 | 1922 | X-RAY DIFFRACTION | r_angle_refined_deg1.594 | 1.632 | 3184 | X-RAY DIFFRACTION | r_angle_other_deg1.403 | 1.571 | 4479 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.154 | 5 | 298 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.299 | 25.167 | 120 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.703 | 15 | 328 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg23.816 | 15 | 3 | X-RAY DIFFRACTION | r_chiral_restr0.072 | 0.2 | 295 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 2736 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 505 | | | | | | | | | | | |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.341 | 97 | - |
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Rwork | 0.331 | 1456 | - |
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all | - | 1553 | - |
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obs | - | - | 97.86 % |
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