Software | Name | Version | Classification |
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HKL-2000 | | data scalingPHENIX | 1.12_2829refinementPDB_EXTRACT | 3.27 | data extractionHKL-2000 | | data reductionAutoSol | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.752→32.151 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2022 | 1379 | 5.04 % |
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Rwork | 0.1798 | 25961 | - |
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obs | 0.181 | 27340 | 99.7 % |
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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: 52.88 Å2 / Biso mean: 21.3846 Å2 / Biso min: 10.24 Å2 |
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Refinement step | Cycle: final / Resolution: 1.752→32.151 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1375 | 0 | 6 | 184 | 1565 |
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Biso mean | - | - | 31.07 | 32.08 | - |
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Num. residues | - | - | - | - | 174 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 1428 | X-RAY DIFFRACTION | f_angle_d0.843 | 1944 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 217 | X-RAY DIFFRACTION | f_plane_restr0.005 | 247 | X-RAY DIFFRACTION | f_dihedral_angle_d2.535 | 1140 | | | | | |
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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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1.7521-1.8147 | 0.2171 | 146 | 0.1961 | 2485 | 98 | 1.8147-1.8873 | 0.2428 | 131 | 0.1959 | 2555 | 100 | 1.8873-1.9732 | 0.2051 | 114 | 0.1851 | 2579 | 100 | 1.9732-2.0772 | 0.2396 | 125 | 0.1827 | 2575 | 100 | 2.0772-2.2074 | 0.2278 | 157 | 0.1736 | 2531 | 100 | 2.2074-2.3777 | 0.2036 | 133 | 0.1753 | 2597 | 100 | 2.3777-2.6169 | 0.1984 | 151 | 0.1805 | 2566 | 100 | 2.6169-2.9954 | 0.196 | 139 | 0.1845 | 2627 | 100 | 2.9954-3.7729 | 0.1961 | 143 | 0.1751 | 2654 | 100 | 3.7729-30 | 0.1828 | 140 | 0.1775 | 2792 | 99 |
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Refinement TLS params. | Method: refined / Origin x: 48.9656 Å / Origin y: 31.7331 Å / Origin z: 37.29 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1065 Å2 | -0.0022 Å2 | -0.0027 Å2 | - | 0.1117 Å2 | 0.0118 Å2 | - | - | 0.1272 Å2 |
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L | 1.2142 °2 | -0.3131 °2 | -0.151 °2 | - | 0.879 °2 | -0.0082 °2 | - | - | 1.481 °2 |
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S | -0.0176 Å ° | -0.06 Å ° | 0.0239 Å ° | 0.0598 Å ° | -0.0177 Å ° | -0.051 Å ° | -0.0366 Å ° | 0.1058 Å ° | 0.0318 Å ° |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | allA1 - 174 | 2 | X-RAY DIFFRACTION | 1 | allA301 - 484 | 3 | X-RAY DIFFRACTION | 1 | allA201 | | | | | | |
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