Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementMOSFLM | | data reductionSCALA | | data scaling | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→50.202 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.87 / Stereochemistry target values: MLHL
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2412 | 1568 | 4.89 % |
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Rwork | 0.2186 | - | - |
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obs | 0.2197 | 32088 | 99.1 % |
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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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Refinement step | Cycle: LAST / Resolution: 2.3→50.202 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4243 | 0 | 2 | 205 | 4450 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 4346 | X-RAY DIFFRACTION | f_angle_d0.94 | 5896 | X-RAY DIFFRACTION | f_dihedral_angle_d15.061 | 1584 | X-RAY DIFFRACTION | f_chiral_restr0.033 | 648 | X-RAY DIFFRACTION | f_plane_restr0.004 | 774 | | | | | |
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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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2.3-2.3742 | 0.3303 | 149 | 0.2792 | 2764 | X-RAY DIFFRACTION | 100 | 2.3742-2.4591 | 0.2832 | 149 | 0.2569 | 2739 | X-RAY DIFFRACTION | 100 | 2.4591-2.5576 | 0.2782 | 140 | 0.2455 | 2760 | X-RAY DIFFRACTION | 100 | 2.5576-2.6739 | 0.2592 | 131 | 0.2571 | 2757 | X-RAY DIFFRACTION | 100 | 2.6739-2.8149 | 0.2729 | 147 | 0.2431 | 2766 | X-RAY DIFFRACTION | 100 | 2.8149-2.9913 | 0.2988 | 135 | 0.2321 | 2785 | X-RAY DIFFRACTION | 100 | 2.9913-3.2222 | 0.2419 | 144 | 0.2195 | 2767 | X-RAY DIFFRACTION | 100 | 3.2222-3.5464 | 0.2311 | 139 | 0.2185 | 2790 | X-RAY DIFFRACTION | 100 | 3.5464-4.0593 | 0.2033 | 151 | 0.2007 | 2783 | X-RAY DIFFRACTION | 100 | 4.0593-5.1135 | 0.2081 | 127 | 0.1763 | 2830 | X-RAY DIFFRACTION | 99 | 5.1135-50.2135 | 0.2331 | 156 | 0.2253 | 2779 | X-RAY DIFFRACTION | 93 |
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Refinement TLS params. | Method: refined / Origin x: 15.6366 Å / Origin y: 55.0312 Å / Origin z: 51.5731 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1529 Å2 | 0.0127 Å2 | 0.0686 Å2 | - | 0.1629 Å2 | -0.0071 Å2 | - | - | 0.1289 Å2 |
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L | 0.4688 °2 | 0.6455 °2 | -0.0991 °2 | - | 1.3784 °2 | -0.2831 °2 | - | - | 0.1889 °2 |
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S | 0.0375 Å ° | 0.0137 Å ° | 0.0452 Å ° | 0.1489 Å ° | 0.0151 Å ° | 0.1115 Å ° | -0.0629 Å ° | -0.0881 Å ° | 0.0058 Å ° |
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Refinement TLS group | Selection details: all |
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