Software | Name | Version | Classification |
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SBC-Collect | | data collectionHKL-3000 | | phasingREFMAC | 5.5.0054refinementHKL-3000 | | data reductionHKL-3000 | | data scaling | | | | | |
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Refinement | Method to determine structure : MAD / Resolution: 2→55.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.649 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.173 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection | Selection details |
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Rfree![](img/lk-wikipe.gif) | 0.2413 | 1128 | 5.1 % | RANDOM |
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Rwork![](img/lk-wikipe.gif) | 0.20282 | - | - | - |
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obs | 0.20479 | 20972 | 98.52 % | - |
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all | - | 21287 | - | - |
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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: 31.506 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.16 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.1 Å2 | 0 Å2 |
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3- | - | - | -0.06 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2→55.99 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2514 | 0 | 5 | 60 | 2579 |
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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_d0.019 | 0.022 | 2559 | X-RAY DIFFRACTION | r_angle_refined_deg1.641 | 1.992 | 3457 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.358 | 5 | 330 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.403 | 24.737 | 95 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.712 | 15 | 464 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.399 | 15 | 14 | X-RAY DIFFRACTION | r_chiral_restr0.119 | 0.2 | 402 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.021 | 1862 | X-RAY DIFFRACTION | r_mcbond_it0.941 | 1.5 | 1646 | X-RAY DIFFRACTION | r_mcangle_it1.723 | 2 | 2653 | X-RAY DIFFRACTION | r_scbond_it2.952 | 3 | 913 | X-RAY DIFFRACTION | r_scangle_it4.777 | 4.5 | 804 | | | | | | | | | | | | |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.266 | 77 | - |
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Rwork | 0.224 | 1492 | - |
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obs | - | 1569 | 97.64 % |
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Refinement TLS params. | Method: refined / Origin x: 115.197 Å / Origin y: -3.298 Å / Origin z: 44.249 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0829 Å2 | 0.0113 Å2 | 0.0049 Å2 | - | 0.0213 Å2 | -0.0135 Å2 | - | - | 0.0328 Å2 |
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L | 1.6167 °2 | -0.4719 °2 | 0.2621 °2 | - | 0.702 °2 | -0.1542 °2 | - | - | 0.9338 °2 |
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S | -0.0459 Å ° | -0.077 Å ° | -0.0302 Å ° | -0.0268 Å ° | 0.0599 Å ° | -0.0312 Å ° | -0.0231 Å ° | 0.0376 Å ° | -0.0139 Å ° |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A1 - 50 | 2 | X-RAY DIFFRACTION | 1 | A51 - 100 | 3 | X-RAY DIFFRACTION | 1 | A101 - 166 | 4 | X-RAY DIFFRACTION | 1 | B-2 - 50 | 5 | X-RAY DIFFRACTION | 1 | B51 - 100 | 6 | X-RAY DIFFRACTION | 1 | B101 - 166 | | | | | | |
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