Software | Name | Version | Classification |
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HKL-2000 | | data collectionSHARP | | phasingPHENIX | (phenix.refine: 1.8.2_1309)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.345→36.068 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7905 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 27.84 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2378 | 1999 | 2.27 % | RANDOM |
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Rwork | 0.2014 | - | - | - |
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all | 0.2032 | 103609 | - | - |
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obs | 0.2022 | 88068 | 85.09 % | - |
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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 max: 155.09 Å2 / Biso mean: 52.4804 Å2 / Biso min: 21.49 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.345→36.068 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10542 | 0 | 0 | 322 | 10864 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.011 | 10734 | X-RAY DIFFRACTION | f_angle_d1.439 | 14562 | X-RAY DIFFRACTION | f_dihedral_angle_d16.54 | 3990 | X-RAY DIFFRACTION | f_chiral_restr0.11 | 1662 | X-RAY DIFFRACTION | f_plane_restr0.007 | 1854 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.3452-2.4038 | 0.3647 | 85 | 0.2796 | 3652 | 3737 | 51 | 2.4038-2.4688 | 0.3275 | 100 | 0.248 | 4294 | 4394 | 59 | 2.4688-2.5414 | 0.325 | 112 | 0.2317 | 4807 | 4919 | 67 | 2.5414-2.6234 | 0.2962 | 124 | 0.2375 | 5357 | 5481 | 74 | 2.6234-2.7172 | 0.2428 | 136 | 0.2529 | 5854 | 5990 | 82 | 2.7172-2.8259 | 0.2945 | 152 | 0.2426 | 6521 | 6673 | 90 | 2.8259-2.9545 | 0.2789 | 161 | 0.2359 | 6959 | 7120 | 96 | 2.9545-3.1102 | 0.2465 | 167 | 0.2349 | 7180 | 7347 | 100 | 3.1102-3.3049 | 0.2853 | 168 | 0.2302 | 7228 | 7396 | 100 | 3.3049-3.5599 | 0.2533 | 167 | 0.21 | 7203 | 7370 | 100 | 3.5599-3.9177 | 0.2698 | 121 | 0.1885 | 5192 | 5313 | 71 | 3.9177-4.4837 | 0.1827 | 168 | 0.1586 | 7231 | 7399 | 100 | 4.4837-5.6455 | 0.1793 | 167 | 0.1521 | 7237 | 7404 | 100 | 5.6455-36.0721 | 0.21 | 171 | 0.2025 | 7354 | 7525 | 100 |
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Refinement TLS params. | Method: refined / Origin x: -36.3957 Å / Origin y: -60.8628 Å / Origin z: -0.2437 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2187 Å2 | -0.0004 Å2 | -0.001 Å2 | - | 0.2166 Å2 | -0.0017 Å2 | - | - | 0.2695 Å2 |
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L | 0.308 °2 | 0.0054 °2 | -0.0311 °2 | - | 0.2684 °2 | -0.0016 °2 | - | - | 0.4044 °2 |
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S | -0.0115 Å ° | 0.0144 Å ° | -0.0107 Å ° | -0.0224 Å ° | -0.0127 Å ° | -0.0028 Å ° | -0.0064 Å ° | 0.0048 Å ° | 0.0215 Å ° |
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Refinement TLS group | Selection details: ALL |
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