Software | Name | Version | Classification |
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HKL-2000 | 2.3.10data scalingPHASER | 2.7.18phasingPHENIX | dev-2611 | refinementPDB_EXTRACT | 3.25 | data extractionHKL-2000 | 2.3.10data reduction | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Computational design model Resolution: 1.8→44.901 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.3 Details: Iterative rounds of manual model building in Coot and refinement in Phenix.
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2264 | 1648 | 10.01 % |
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Rwork | 0.2012 | - | - |
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obs | 0.2038 | 16463 | 94.31 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 115.73 Å2 / Biso mean: 41.0369 Å2 / Biso min: 19.71 Å2 |
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Refinement step | Cycle: final / Resolution: 1.8→44.901 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1413 | 0 | 1 | 97 | 1511 |
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Biso mean | - | - | 53.79 | 43.91 | - |
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Num. residues | - | - | - | - | 196 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.003 | 1446 | X-RAY DIFFRACTION | f_angle_d0.491 | 1963 | X-RAY DIFFRACTION | f_chiral_restr0.035 | 249 | X-RAY DIFFRACTION | f_plane_restr0.004 | 257 | X-RAY DIFFRACTION | f_dihedral_angle_d14.785 | 932 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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1.8-1.853 | 0.3679 | 109 | 0.3059 | 1028 | 79 | 1.853-1.9128 | 0.2624 | 121 | 0.2886 | 1074 | 83 | 1.9128-1.9811 | 0.2964 | 121 | 0.256 | 1116 | 88 | 1.9811-2.0605 | 0.2987 | 132 | 0.2367 | 1202 | 93 | 2.0605-2.1542 | 0.2134 | 137 | 0.2033 | 1238 | 97 | 2.1542-2.2678 | 0.2458 | 144 | 0.1867 | 1266 | 98 | 2.2678-2.4099 | 0.2342 | 142 | 0.1932 | 1271 | 97 | 2.4099-2.5959 | 0.2226 | 145 | 0.2 | 1272 | 98 | 2.5959-2.8571 | 0.1932 | 144 | 0.1859 | 1280 | 99 | 2.8571-3.2705 | 0.2286 | 148 | 0.2039 | 1318 | 99 | 3.2705-4.12 | 0.2129 | 148 | 0.1725 | 1340 | 100 | 4.12-44.901 | 0.2194 | 157 | 0.2095 | 1410 | 100 |
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Refinement TLS params. | Method: refined / Origin x: 31.6084 Å / Origin y: 20.8636 Å / Origin z: 51.2367 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2139 Å2 | 0.0005 Å2 | 0.0266 Å2 | - | 0.2269 Å2 | 0.0117 Å2 | - | - | 0.2198 Å2 |
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L | 0.7929 °2 | -0.0755 °2 | 0.0316 °2 | - | 1.8716 °2 | 0.3544 °2 | - | - | 0.7995 °2 |
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S | 0.1566 Å ° | -0.0159 Å ° | 0.0387 Å ° | -0.0884 Å ° | -0.1626 Å ° | -0.1147 Å ° | -0.0546 Å ° | -0.0411 Å ° | -0.0001 Å ° |
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Refinement TLS group | Selection details: (chain 'A' and resid 9 through 204) |
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