Software | Name | Version | Classification |
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CBASS | | data collectionSHELXS | | phasingREFMAC | 5 | refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | |
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Refinement | Method to determine structure: SAD Starting model: 1DNS Resolution: 1.3→30.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.656 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / 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 | 0.21884 | 256 | 4.6 % | RANDOM |
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Rwork | 0.19672 | - | - | - |
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all | 0.19769 | 5574 | - | - |
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obs | - | 5301 | 95.11 % | - |
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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: 12.795 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.09 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.09 Å2 | 0 Å2 |
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3- | - | - | 0.17 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.056 Å | 0.055 Å |
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Refinement step | Cycle: LAST / Resolution: 1.3→30.56 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 163 | 0 | 30 | 193 |
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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 | 180 | X-RAY DIFFRACTION | r_angle_refined_deg1.6 | 3 | 270 | X-RAY DIFFRACTION | r_chiral_restr0.068 | 0.2 | 31 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 83 | X-RAY DIFFRACTION | r_nbd_refined0.36 | 0.2 | 69 | X-RAY DIFFRACTION | r_nbtor_refined0.282 | 0.2 | 106 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.106 | 0.2 | 20 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.194 | 0.2 | 21 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.071 | 0.2 | 11 | X-RAY DIFFRACTION | r_scbond_it0.832 | 3 | 259 | X-RAY DIFFRACTION | r_scangle_it1.272 | 4.5 | 270 | | | | | | | | | | | |
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LS refinement shell | Resolution: 1.303→1.336 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.426 | 6 | - |
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Rwork | 0.47 | 249 | - |
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obs | - | - | 62.04 % |
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Refinement TLS params. | Method: refined / Origin x: 11.4162 Å / Origin y: 12.7391 Å / Origin z: 2.3922 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0418 Å2 | 0.0001 Å2 | -0.0099 Å2 | - | 0.0201 Å2 | -0.0003 Å2 | - | - | 0.025 Å2 |
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L | 0.7644 °2 | -0.9107 °2 | -0.0164 °2 | - | 2.6011 °2 | -0.3799 °2 | - | - | 0.1056 °2 |
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S | -0.0447 Å ° | -0.014 Å ° | -0.0434 Å ° | 0.2121 Å ° | 0.0378 Å ° | -0.0153 Å ° | 0.003 Å ° | 0.0553 Å ° | 0.0068 Å ° |
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