Software | Name | Version | Classification |
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CBASS | | data collectionPHASES | | phasingREFMAC | 5.2.0019refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DNS Resolution: 1.3→30.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.984 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2224 | 246 | 4.6 % | RANDOM |
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Rwork | 0.20164 | - | - | - |
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obs | 0.2026 | 5117 | 91.05 % | - |
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all | - | 5612 | - | - |
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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 mean: 13.098 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.25 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.25 Å2 | 0 Å2 |
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3- | - | - | 0.5 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.061 Å | 0.06 Å |
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Refinement step | Cycle: LAST / Resolution: 1.3→30.4 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 163 | 1 | 42 | 206 |
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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_d0.006 | 0.021 | 182 | X-RAY DIFFRACTION | r_angle_refined_deg1.251 | 3 | 278 | X-RAY DIFFRACTION | r_chiral_restr0.06 | 0.2 | 32 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 83 | X-RAY DIFFRACTION | r_nbd_refined0.158 | 0.2 | 59 | X-RAY DIFFRACTION | r_nbtor_refined0.276 | 0.2 | 108 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.151 | 0.2 | 28 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.187 | 0.2 | 19 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.088 | 0.2 | 15 | X-RAY DIFFRACTION | r_scbond_it0.895 | 3 | 261 | X-RAY DIFFRACTION | r_scangle_it1.318 | 4.5 | 278 | | | | | | | | | | | |
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LS refinement shell | Resolution: 1.3→1.332 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.423 | 13 | - |
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Rwork | 0.396 | 174 | - |
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obs | - | - | 43.9 % |
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Refinement TLS params. | Method: refined / Origin x: 11.4486 Å / Origin y: 12.577 Å / Origin z: 2.4137 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0704 Å2 | -0.0063 Å2 | -0.0152 Å2 | - | 0.0549 Å2 | 0.0005 Å2 | - | - | 0.0671 Å2 |
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L | 0.9159 °2 | -1.0744 °2 | 0.1786 °2 | - | 3.9115 °2 | -0.8824 °2 | - | - | 0.4272 °2 |
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S | -0.0595 Å ° | -0.0351 Å ° | -0.0042 Å ° | 0.2754 Å ° | 0.0474 Å ° | -0.0337 Å ° | -0.0654 Å ° | 0.047 Å ° | 0.012 Å ° |
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