Software | Name | Version | Classification |
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SBC-Collect | | data collectionSHELXD | | phasingMLPHARE | | phasingDM | | model buildingARP | | model buildingWARP | | model buildingHKL-3000 | | phasingPHENIX | (phenix.refine: 1.6.4_486)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingDM | | phasing | | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.383→37.076 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 17.8 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1851 | 2141 | 5.05 % | random |
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Rwork | 0.1634 | - | - | - |
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obs | 0.1645 | 42410 | 95.9 % | - |
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all | - | 42410 | - | - |
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.231 Å2 / ksol: 0.375 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.4919 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 0.3151 Å2 | 0 Å2 |
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3- | - | - | -3.807 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.383→37.076 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1897 | 0 | 24 | 299 | 2220 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 2043 | X-RAY DIFFRACTION | f_angle_d1.178 | 2815 | X-RAY DIFFRACTION | f_dihedral_angle_d11.945 | 762 | X-RAY DIFFRACTION | f_chiral_restr0.073 | 317 | X-RAY DIFFRACTION | f_plane_restr0.009 | 380 | | | | | |
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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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1.383-1.4324 | 0.2782 | 177 | 0.257 | 3433 | X-RAY DIFFRACTION | 83 | 1.4324-1.4898 | 0.2695 | 192 | 0.2226 | 3743 | X-RAY DIFFRACTION | 90 | 1.4898-1.5576 | 0.2369 | 209 | 0.1904 | 3899 | X-RAY DIFFRACTION | 94 | 1.5576-1.6397 | 0.1879 | 220 | 0.1637 | 3961 | X-RAY DIFFRACTION | 96 | 1.6397-1.7424 | 0.2024 | 221 | 0.1614 | 4063 | X-RAY DIFFRACTION | 98 | 1.7424-1.877 | 0.1744 | 215 | 0.1622 | 4141 | X-RAY DIFFRACTION | 99 | 1.877-2.0658 | 0.1799 | 240 | 0.1565 | 4138 | X-RAY DIFFRACTION | 100 | 2.0658-2.3647 | 0.1664 | 226 | 0.1596 | 4209 | X-RAY DIFFRACTION | 100 | 2.3647-2.9791 | 0.1901 | 213 | 0.1688 | 4252 | X-RAY DIFFRACTION | 100 | 2.9791-37.0892 | 0.1706 | 228 | 0.1495 | 4430 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: 47.8165 Å / Origin y: 10.1777 Å / Origin z: 5.0956 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1088 Å2 | -0.0034 Å2 | 0.0003 Å2 | - | 0.1148 Å2 | 0.0009 Å2 | - | - | 0.1128 Å2 |
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L | 0.1188 °2 | 0.0398 °2 | -0.0017 °2 | - | 0.2175 °2 | 0.0767 °2 | - | - | 0.0361 °2 |
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S | 0.0167 Å ° | -0.0054 Å ° | 0.0086 Å ° | 0.0023 Å ° | -0.0082 Å ° | 0.0049 Å ° | -0.0002 Å ° | 0.0024 Å ° | -0.0043 Å ° |
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Refinement TLS group | Selection details: chain A |
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