Software | Name | Version | Classification |
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SBC-Collect | | data collectionHKL-3000 | | phasingREFMAC | 5.5.0102refinementHKL-3000 | | data reductionHKL-3000 | | data scaling | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→75.11 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / SU B: 21.602 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.259 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.26308 | 369 | 4.6 % | RANDOM |
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Rwork | 0.22569 | - | - | - |
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obs | 0.22745 | 7687 | 99.13 % | - |
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all | - | 7754 | - | - |
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK |
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Displacement parameters | Biso mean: 31.88 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.99 Å2 | -0.99 Å2 | 0 Å2 |
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2- | - | -1.99 Å2 | 0 Å2 |
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3- | - | - | 2.98 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.5→75.11 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1125 | 0 | 0 | 23 | 1148 |
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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_d0.022 | 0.022 | 1148 | X-RAY DIFFRACTION | r_angle_refined_deg2.127 | 1.969 | 1559 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg8.796 | 5 | 143 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg38.028 | 24.151 | 53 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg21.084 | 15 | 188 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.334 | 15 | 8 | X-RAY DIFFRACTION | r_chiral_restr0.156 | 0.2 | 176 | X-RAY DIFFRACTION | r_gen_planes_refined0.01 | 0.021 | 877 | X-RAY DIFFRACTION | r_mcbond_it1.225 | 1.5 | 723 | X-RAY DIFFRACTION | r_mcangle_it2.262 | 2 | 1158 | X-RAY DIFFRACTION | r_scbond_it2.846 | 3 | 425 | X-RAY DIFFRACTION | r_scangle_it4.754 | 4.5 | 401 | | | | | | | | | | | | |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.406 | 27 | - |
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Rwork | 0.328 | 503 | - |
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obs | - | 530 | 92.98 % |
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Refinement TLS params. | Method: refined / Origin x: -2.7558 Å / Origin y: 29.5146 Å / Origin z: 3.8747 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1758 Å2 | 0.0279 Å2 | 0.0088 Å2 | - | 0.2511 Å2 | -0.0174 Å2 | - | - | 0.2861 Å2 |
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L | 5.844 °2 | -3.7607 °2 | -3.5666 °2 | - | 4.0592 °2 | 1.6562 °2 | - | - | 4.1715 °2 |
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S | -0.152 Å ° | -0.1078 Å ° | -0.0708 Å ° | -0.1609 Å ° | 0.1277 Å ° | 0.1353 Å ° | -0.0047 Å ° | 0.2252 Å ° | 0.0243 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 | A0 - 26 | 2 | X-RAY DIFFRACTION | 1 | A39 - 70 | 3 | X-RAY DIFFRACTION | 1 | A71 - 100 | 4 | X-RAY DIFFRACTION | 1 | A101 - 130 | 5 | X-RAY DIFFRACTION | 1 | A131 - 152 | | | | | |
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