Software | Name | Version | Classification |
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REFMAC | 5.8.0267refinementPDB_EXTRACT | 3.27 | data extractionautoPROC | | data reductionSTARANISO | | data scalingMOLREP | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7TBN Resolution: 2.32→50.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.889 / SU B: 13.013 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.405 / 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 | 0.2839 | 1136 | 5 % | RANDOM |
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Rwork | 0.1962 | - | - | - |
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obs | 0.2008 | 21423 | 61.06 % | - |
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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: 168.23 Å2 / Biso mean: 59.333 Å2 / Biso min: 19.24 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.78 Å2 | 0.27 Å2 | -0.01 Å2 |
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2- | - | 0.48 Å2 | -0.75 Å2 |
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3- | - | - | 0.53 Å2 |
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Refinement step | Cycle: final / Resolution: 2.32→50.01 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5322 | 0 | 12 | 282 | 5616 |
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Biso mean | - | - | 66.21 | 45.38 | - |
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Num. residues | - | - | - | - | 677 |
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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 | 5434 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.017 | 5300 | X-RAY DIFFRACTION | r_angle_refined_deg1.691 | 1.638 | 7339 | X-RAY DIFFRACTION | r_angle_other_deg1.223 | 1.588 | 12224 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.551 | 5 | 679 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.154 | 24.089 | 291 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg19.762 | 15 | 1005 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.178 | 15 | 28 | X-RAY DIFFRACTION | r_chiral_restr0.063 | 0.2 | 708 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 6175 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1149 | | | | | | | | | | | |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 10821 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05 |
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LS refinement shell | Resolution: 2.321→2.381 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.13 | 2 | - |
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Rwork | 0.245 | 59 | - |
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all | - | 61 | - |
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obs | - | - | 2.27 % |
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