Software | Name | Version | Classification |
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Blu-Ice | | data collectionPHENIX | - AutoSol - Solve | model buildingPHENIX | (phenix.refine: dev_572)refinementHKL-2000 | | data reductionHKL-2000 | | data scalingPHENIX | - AutoSol - Solve | phasing | | | | | | |
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Refinement | Method to determine structure: MAD / Resolution: 1.651→19.378 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 19.35 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1925 | 1949 | 4.04 % | random |
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Rwork | 0.1633 | - | - | - |
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obs | 0.1645 | 48256 | 96.84 % | - |
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all | - | 48256 | - | - |
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.114 Å2 / ksol: 0.37 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.152 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.9859 Å2 | 0 Å2 |
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3- | - | - | 2.5842 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.651→19.378 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2535 | 0 | 0 | 331 | 2866 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 2585 | X-RAY DIFFRACTION | f_angle_d1.065 | 3531 | X-RAY DIFFRACTION | f_dihedral_angle_d13.945 | 883 | X-RAY DIFFRACTION | f_chiral_restr0.08 | 418 | X-RAY DIFFRACTION | f_plane_restr0.003 | 459 | | | | | |
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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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1.6511-1.71 | 0.345 | 182 | 0.3014 | 4230 | X-RAY DIFFRACTION | 89 | 1.71-1.7785 | 0.2797 | 185 | 0.2396 | 4382 | X-RAY DIFFRACTION | 93 | 1.7785-1.8593 | 0.252 | 187 | 0.1855 | 4442 | X-RAY DIFFRACTION | 94 | 1.8593-1.9573 | 0.1915 | 196 | 0.1485 | 4580 | X-RAY DIFFRACTION | 96 | 1.9573-2.0798 | 0.1947 | 196 | 0.138 | 4647 | X-RAY DIFFRACTION | 98 | 2.0798-2.2402 | 0.1932 | 197 | 0.1342 | 4709 | X-RAY DIFFRACTION | 99 | 2.2402-2.4652 | 0.1746 | 197 | 0.1373 | 4735 | X-RAY DIFFRACTION | 99 | 2.4652-2.821 | 0.2129 | 198 | 0.1682 | 4774 | X-RAY DIFFRACTION | 99 | 2.821-3.5505 | 0.183 | 202 | 0.1619 | 4827 | X-RAY DIFFRACTION | 100 | 3.5505-19.3796 | 0.163 | 209 | 0.1624 | 4981 | X-RAY DIFFRACTION | 99 |
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