Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementHKL-2000 | | data scalingPDB_EXTRACT | 3.15 | data extractionHKL-2000 | | data reductionPHENIX | | phasing | | | | | |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5H9L Resolution: 1.441→33.36 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.38 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1882 | 1190 | 4.82 % |
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Rwork | 0.1598 | 23506 | - |
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obs | 0.1612 | 24696 | 98.83 % |
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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: 56.54 Å2 / Biso mean: 16.8489 Å2 / Biso min: 4.94 Å2 |
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Refinement step | Cycle: final / Resolution: 1.441→33.36 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1184 | 0 | 34 | 228 | 1446 |
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Biso mean | - | - | 20.32 | 28.28 | - |
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Num. residues | - | - | - | - | 156 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 1253 | X-RAY DIFFRACTION | f_angle_d1.08 | 1686 | X-RAY DIFFRACTION | f_chiral_restr0.04 | 184 | X-RAY DIFFRACTION | f_plane_restr0.004 | 223 | X-RAY DIFFRACTION | f_dihedral_angle_d13.074 | 453 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.4407-1.4984 | 0.1843 | 115 | 0.1794 | 2546 | 2661 | 96 | 1.4984-1.5666 | 0.2061 | 144 | 0.1663 | 2575 | 2719 | 99 | 1.5666-1.6492 | 0.2213 | 135 | 0.1681 | 2599 | 2734 | 99 | 1.6492-1.7525 | 0.1912 | 137 | 0.1667 | 2600 | 2737 | 99 | 1.7525-1.8878 | 0.205 | 140 | 0.164 | 2620 | 2760 | 99 | 1.8878-2.0778 | 0.193 | 133 | 0.1568 | 2615 | 2748 | 99 | 2.0778-2.3783 | 0.1967 | 126 | 0.1585 | 2629 | 2755 | 99 | 2.3783-2.9962 | 0.1821 | 129 | 0.1732 | 2651 | 2780 | 99 | 2.9962-33.3688 | 0.1695 | 131 | 0.1454 | 2671 | 2802 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -6.2796 Å / Origin y: 5.9056 Å / Origin z: -10.0547 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0594 Å2 | 0.0027 Å2 | -0.0072 Å2 | - | 0.0606 Å2 | -0.0102 Å2 | - | - | 0.0617 Å2 |
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L | 0.8893 °2 | 0.1577 °2 | -0.3351 °2 | - | 1.2438 °2 | -0.1686 °2 | - | - | 2.3673 °2 |
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S | -0.0437 Å ° | -0.028 Å ° | -0.0182 Å ° | 0.0537 Å ° | 0.0198 Å ° | -0.0282 Å ° | 0.0797 Å ° | -0.0348 Å ° | 0.0206 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 - 156 | 2 | X-RAY DIFFRACTION | 1 | allB1 | 3 | X-RAY DIFFRACTION | 1 | allS1 - 269 | | | | | | |
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