Software | Name | Version | Classification |
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HKL-3000 | | data scalingPHENIX | 1.18.2-3874-000 | refinementPDB_EXTRACT | | data extractionHKL-3000 | | data reductionPHENIX | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.71 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 23.29 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2518 | 1406 | 10.04 % |
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Rwork | 0.2194 | - | - |
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obs | 0.2226 | 14006 | 99.85 % |
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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: 2.2→24.71 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1675 | 0 | 0 | 54 | 1729 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 1724 | X-RAY DIFFRACTION | f_angle_d1.068 | 2336 | X-RAY DIFFRACTION | f_dihedral_angle_d5.704 | 235 | X-RAY DIFFRACTION | f_chiral_restr0.054 | 225 | X-RAY DIFFRACTION | f_plane_restr0.007 | 324 | | | | | |
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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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2.2-2.28 | 0.2927 | 144 | 0.2447 | 1223 | X-RAY DIFFRACTION | 100 | 2.28-2.37 | 0.2866 | 132 | 0.2359 | 1250 | X-RAY DIFFRACTION | 100 | 2.37-2.48 | 0.2537 | 137 | 0.2372 | 1233 | X-RAY DIFFRACTION | 100 | 2.48-2.61 | 0.2971 | 141 | 0.2444 | 1234 | X-RAY DIFFRACTION | 100 | 2.61-2.77 | 0.2843 | 136 | 0.2368 | 1251 | X-RAY DIFFRACTION | 100 | 2.77-2.98 | 0.2835 | 144 | 0.2491 | 1237 | X-RAY DIFFRACTION | 100 | 2.98-3.28 | 0.272 | 138 | 0.2578 | 1256 | X-RAY DIFFRACTION | 100 | 3.28-3.76 | 0.2686 | 138 | 0.2244 | 1263 | X-RAY DIFFRACTION | 100 | 3.76-4.73 | 0.1889 | 141 | 0.1776 | 1297 | X-RAY DIFFRACTION | 100 | 4.73-24.71 | 0.2441 | 155 | 0.2078 | 1356 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: -20.2273 Å / Origin y: 13.4228 Å / Origin z: -10.8553 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2307 Å2 | 0.0028 Å2 | -0.0512 Å2 | - | 0.2784 Å2 | -0.0602 Å2 | - | - | 0.2415 Å2 |
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L | 0.0916 °2 | 0.106 °2 | -0.0142 °2 | - | 1.3292 °2 | -0.2358 °2 | - | - | 0.242 °2 |
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S | 0.08 Å ° | -0.0771 Å ° | 0.0417 Å ° | 0.1001 Å ° | -0.1176 Å ° | 0.0059 Å ° | -0.0248 Å ° | -0.0678 Å ° | -0.0006 Å ° |
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Refinement TLS group | Selection details: all |
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