Software | Name | Version | Classification |
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HKL-2000 | | data collectionSOLVE | | phasingPHENIX | (phenix.refine: 1.7.3_928)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure : SAD / Resolution: 2.35→40.838 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 25.38 / Stereochemistry target values: ML
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection |
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Rfree![](img/lk-wikipe.gif) | 0.2272 | 1450 | 4.94 % |
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Rwork![](img/lk-wikipe.gif) | 0.1889 | - | - |
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obs | 0.1908 | 29358 | 81.28 % |
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all | - | 29358 | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.454 Å2 / ksol: 0.353 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.199 Å2 | 0 Å2 | -1.2042 Å2 |
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2- | - | 0.3841 Å2 | 0 Å2 |
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3- | - | - | -0.5831 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.35→40.838 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2536 | 634 | 17 | 347 | 3534 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 3330 | X-RAY DIFFRACTION | f_angle_d1.275 | 4639 | X-RAY DIFFRACTION | f_dihedral_angle_d22.456 | 1281 | X-RAY DIFFRACTION | f_chiral_restr0.075 | 509 | X-RAY DIFFRACTION | f_plane_restr0.005 | 485 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.3502-2.4342 | 0.2149 | 67 | 0.2106 | 1397 | X-RAY DIFFRACTION | 41 | 2.4342-2.5317 | 0.2781 | 103 | 0.2103 | 1887 | X-RAY DIFFRACTION | 56 | 2.5317-2.6469 | 0.2491 | 113 | 0.2328 | 2197 | X-RAY DIFFRACTION | 64 | 2.6469-2.7864 | 0.2961 | 121 | 0.2258 | 2454 | X-RAY DIFFRACTION | 71 | 2.7864-2.9609 | 0.2777 | 176 | 0.2382 | 2898 | X-RAY DIFFRACTION | 85 | 2.9609-3.1894 | 0.2904 | 177 | 0.2295 | 3334 | X-RAY DIFFRACTION | 98 | 3.1894-3.5103 | 0.2189 | 172 | 0.1834 | 3421 | X-RAY DIFFRACTION | 99 | 3.5103-4.0178 | 0.2204 | 178 | 0.1718 | 3402 | X-RAY DIFFRACTION | 100 | 4.0178-5.0605 | 0.1839 | 165 | 0.1454 | 3449 | X-RAY DIFFRACTION | 99 | 5.0605-40.8443 | 0.1962 | 178 | 0.1868 | 3469 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: refined / Origin x: -31.3488 Å / Origin y: 3.2584 Å / Origin z: 27.7841 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0945 Å2 | 0.0239 Å2 | -0.0489 Å2 | - | 0.1335 Å2 | -0.0266 Å2 | - | - | 0.0694 Å2 |
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L | 3.1071 °2 | 0.35 °2 | -0.5594 °2 | - | 3.5711 °2 | -0.0022 °2 | - | - | 0.8608 °2 |
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S | 0.1451 Å ° | 0.2354 Å ° | -0.0138 Å ° | -0.1209 Å ° | -0.0959 Å ° | 0.7532 Å ° | -0.0215 Å ° | -0.0888 Å ° | -0.0339 Å ° |
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Refinement TLS group | Selection details: all |
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