Software | Name | Version | Classification |
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PHENIX | 1.17.1_3660refinementHKL-3000 | | data reductionHKL-3000 | | data scalingPHENIX | 1.12-2829 | phasing | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→48.92 Å / SU ML: 0.2823 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.1392 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2372 | 1565 | 5.03 % |
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Rwork | 0.1959 | 29530 | - |
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obs | 0.1981 | 31095 | 98.41 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 41.45 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.3→48.92 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5979 | 0 | 36 | 203 | 6218 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0024 | 6149 | X-RAY DIFFRACTION | f_angle_d0.5407 | 8334 | X-RAY DIFFRACTION | f_chiral_restr0.0407 | 970 | X-RAY DIFFRACTION | f_plane_restr0.0038 | 1080 | X-RAY DIFFRACTION | f_dihedral_angle_d19.2437 | 871 | | | | | |
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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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2.3-2.37 | 0.3018 | 133 | 0.2419 | 2553 | X-RAY DIFFRACTION | 92.91 | 2.37-2.46 | 0.2912 | 132 | 0.2355 | 2683 | X-RAY DIFFRACTION | 98.77 | 2.46-2.56 | 0.2837 | 135 | 0.2257 | 2662 | X-RAY DIFFRACTION | 98.69 | 2.56-2.67 | 0.3238 | 151 | 0.2246 | 2698 | X-RAY DIFFRACTION | 99.13 | 2.67-2.81 | 0.2792 | 126 | 0.23 | 2678 | X-RAY DIFFRACTION | 98.49 | 2.81-2.99 | 0.2669 | 147 | 0.2186 | 2681 | X-RAY DIFFRACTION | 99.23 | 2.99-3.22 | 0.2625 | 157 | 0.2147 | 2718 | X-RAY DIFFRACTION | 99.27 | 3.22-3.55 | 0.2445 | 133 | 0.1986 | 2727 | X-RAY DIFFRACTION | 99.41 | 3.55-4.06 | 0.2399 | 138 | 0.1758 | 2708 | X-RAY DIFFRACTION | 98.85 | 4.06-5.11 | 0.1739 | 159 | 0.1585 | 2714 | X-RAY DIFFRACTION | 99.65 | 5.11-48.92 | 0.2021 | 154 | 0.1804 | 2708 | X-RAY DIFFRACTION | 98.15 |
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Refinement TLS params. | Method: refined / Origin x: 5.8035089598 Å / Origin y: 81.3786431003 Å / Origin z: 34.3324892463 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.178982137987 Å2 | 0.0214792795713 Å2 | 0.000313831701674 Å2 | - | 0.214789106524 Å2 | 0.0127601396873 Å2 | - | - | 0.268042015808 Å2 |
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L | 0.0694399382609 °2 | 0.190599731558 °2 | 0.264386135592 °2 | - | 0.556959547335 °2 | 0.535552392295 °2 | - | - | 1.06891857357 °2 |
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S | -0.0359532255146 Å ° | 0.00387262317118 Å ° | 0.00825635273862 Å ° | -0.0790544090345 Å ° | -0.0332725563688 Å ° | 0.0809967185201 Å ° | -0.0919540682574 Å ° | -0.00142874573275 Å ° | 0.0767028719483 Å ° |
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Refinement TLS group | Selection details: all |
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