Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.592→38.82 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 16.67 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1935 | 1675 | 5.1 % |
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Rwork | 0.1545 | - | - |
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obs | 0.1564 | 33153 | 99.92 % |
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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: 14.7 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.592→38.82 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2062 | 0 | 17 | 284 | 2363 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.01 | 2233 | X-RAY DIFFRACTION | f_angle_d1.283 | 3057 | X-RAY DIFFRACTION | f_dihedral_angle_d13.532 | 800 | X-RAY DIFFRACTION | f_chiral_restr0.077 | 350 | X-RAY DIFFRACTION | f_plane_restr0.006 | 404 | | | | | |
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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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1.592-1.6389 | 0.2836 | 139 | 0.258 | 2554 | X-RAY DIFFRACTION | 100 | 1.6389-1.6918 | 0.2801 | 159 | 0.2298 | 2546 | X-RAY DIFFRACTION | 100 | 1.6918-1.7523 | 0.2242 | 137 | 0.2157 | 2568 | X-RAY DIFFRACTION | 100 | 1.7523-1.8224 | 0.234 | 135 | 0.1827 | 2576 | X-RAY DIFFRACTION | 100 | 1.8224-1.9054 | 0.2052 | 139 | 0.1583 | 2576 | X-RAY DIFFRACTION | 100 | 1.9054-2.0058 | 0.1695 | 127 | 0.1329 | 2612 | X-RAY DIFFRACTION | 100 | 2.0058-2.1315 | 0.1617 | 133 | 0.1294 | 2597 | X-RAY DIFFRACTION | 100 | 2.1315-2.296 | 0.1938 | 160 | 0.1257 | 2590 | X-RAY DIFFRACTION | 100 | 2.296-2.527 | 0.1782 | 139 | 0.1351 | 2625 | X-RAY DIFFRACTION | 100 | 2.527-2.8926 | 0.1733 | 132 | 0.14 | 2666 | X-RAY DIFFRACTION | 100 | 2.8926-3.6439 | 0.1639 | 141 | 0.1399 | 2692 | X-RAY DIFFRACTION | 100 | 3.6439-38.8311 | 0.2095 | 134 | 0.166 | 2876 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: refined / Origin x: 22.349 Å / Origin y: 1.1728 Å / Origin z: 12.1545 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0651 Å2 | 0.01 Å2 | -0.0022 Å2 | - | 0.055 Å2 | -0.0006 Å2 | - | - | 0.0435 Å2 |
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L | 0.8541 °2 | -0 °2 | -0.0026 °2 | - | 0.8879 °2 | -0.1175 °2 | - | - | 0.8455 °2 |
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S | 0.007 Å ° | -0.0763 Å ° | -0.0268 Å ° | 0.0606 Å ° | 0.0047 Å ° | -0.0469 Å ° | 0.0465 Å ° | 0.0603 Å ° | -0.0101 Å ° |
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Refinement TLS group | Selection details: ALL |
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