Software | Name | Version | Classification |
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PHENIX | (1.14_3260: ???)refinementHKL-2000 | | data reductionHKL-2000 | | data scalingPHENIX | | phasing | | | | |
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Refinement | Resolution: 2.113→30.927 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.55
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.253 | 2000 | 6.23 % |
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Rwork | 0.2055 | - | - |
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obs | 0.2084 | 32104 | 97.7 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Refinement step | Cycle: LAST / Resolution: 2.113→30.927 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3701 | 0 | 34 | 120 | 3855 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 3827 | X-RAY DIFFRACTION | f_angle_d0.89 | 5199 | X-RAY DIFFRACTION | f_dihedral_angle_d21.1 | 1392 | X-RAY DIFFRACTION | f_chiral_restr0.052 | 549 | X-RAY DIFFRACTION | f_plane_restr0.006 | 678 | | | | | |
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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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2.1134-2.1662 | 0.3689 | 133 | 0.272 | 2012 | X-RAY DIFFRACTION | 93 | 2.1662-2.2248 | 0.306 | 135 | 0.2706 | 2023 | X-RAY DIFFRACTION | 95 | 2.2248-2.2902 | 0.3318 | 135 | 0.2563 | 2024 | X-RAY DIFFRACTION | 95 | 2.2902-2.3641 | 0.3379 | 134 | 0.2579 | 2032 | X-RAY DIFFRACTION | 95 | 2.3641-2.4486 | 0.2557 | 137 | 0.2503 | 2067 | X-RAY DIFFRACTION | 96 | 2.4486-2.5466 | 0.3219 | 140 | 0.2588 | 2104 | X-RAY DIFFRACTION | 97 | 2.5466-2.6624 | 0.3125 | 141 | 0.2461 | 2109 | X-RAY DIFFRACTION | 98 | 2.6624-2.8027 | 0.3137 | 143 | 0.2398 | 2160 | X-RAY DIFFRACTION | 99 | 2.8027-2.9782 | 0.3082 | 144 | 0.2355 | 2185 | X-RAY DIFFRACTION | 100 | 2.9782-3.2079 | 0.3021 | 146 | 0.2244 | 2184 | X-RAY DIFFRACTION | 100 | 3.2079-3.5303 | 0.2599 | 147 | 0.2058 | 2216 | X-RAY DIFFRACTION | 100 | 3.5303-4.0402 | 0.2499 | 149 | 0.1702 | 2235 | X-RAY DIFFRACTION | 100 | 4.0402-5.0866 | 0.1931 | 151 | 0.1604 | 2290 | X-RAY DIFFRACTION | 100 | 5.0866-30.9308 | 0.2046 | 165 | 0.1956 | 2463 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: -1.6198 Å / Origin y: 41.9623 Å / Origin z: 167.5249 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.5596 Å2 | 0.1178 Å2 | -0.1975 Å2 | - | 0.2686 Å2 | 0.0008 Å2 | - | - | 0.3933 Å2 |
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L | 2.2211 °2 | 0.9488 °2 | 0.182 °2 | - | 2.2128 °2 | 0.3249 °2 | - | - | 1.6832 °2 |
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S | 0.3477 Å ° | -0.0498 Å ° | -0.3835 Å ° | 0.7782 Å ° | 0.1029 Å ° | -0.4612 Å ° | 0.1811 Å ° | 0.1121 Å ° | -0.2764 Å ° |
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Refinement TLS group | Selection details: all |
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