Software | Name | Version | Classification |
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SBC-Collect | | data collectionHKL-3000 | | data collectionHKL-3000 | | phasingSHELXS | | phasingMLPHARE | | phasingRESOLVE | | model buildingSOLVE | | phasingPHENIX | (phenix.refine: 1.6.2_432)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingRESOLVE | | phasing | | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.907→30.578 Å / SU ML: 0.19 / Isotropic thermal model: mixed / σ(F): 1.33 / Phase error: 19.63 / Stereochemistry target values: MLHL
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1947 | 1446 | 5.06 % |
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Rwork | 0.1603 | - | - |
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obs | 0.162 | 28572 | 99.11 % |
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all | - | 28572 | - |
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.143 Å2 / ksol: 0.373 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.8067 Å2 | 0 Å2 | -6.2234 Å2 |
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2- | - | -4.9579 Å2 | -0 Å2 |
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3- | - | - | 6.7646 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.907→30.578 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2668 | 0 | 0 | 305 | 2973 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.011 | 2746 | X-RAY DIFFRACTION | f_angle_d1.194 | 3726 | X-RAY DIFFRACTION | f_dihedral_angle_d13.851 | 1027 | X-RAY DIFFRACTION | f_chiral_restr0.083 | 418 | X-RAY DIFFRACTION | f_plane_restr0.005 | 484 | | | | | |
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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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1.9073-1.9755 | 0.2669 | 145 | 0.2324 | 2579 | X-RAY DIFFRACTION | 95 | 1.9755-2.0546 | 0.2449 | 143 | 0.1795 | 2697 | X-RAY DIFFRACTION | 99 | 2.0546-2.1481 | 0.2113 | 133 | 0.1708 | 2716 | X-RAY DIFFRACTION | 100 | 2.1481-2.2613 | 0.2251 | 155 | 0.1567 | 2718 | X-RAY DIFFRACTION | 99 | 2.2613-2.4029 | 0.2203 | 132 | 0.1594 | 2708 | X-RAY DIFFRACTION | 100 | 2.4029-2.5884 | 0.2053 | 159 | 0.1603 | 2711 | X-RAY DIFFRACTION | 100 | 2.5884-2.8487 | 0.1881 | 126 | 0.162 | 2744 | X-RAY DIFFRACTION | 100 | 2.8487-3.2605 | 0.1989 | 154 | 0.1616 | 2729 | X-RAY DIFFRACTION | 100 | 3.2605-4.1063 | 0.1601 | 160 | 0.1454 | 2735 | X-RAY DIFFRACTION | 100 | 4.1063-30.5818 | 0.1633 | 139 | 0.1473 | 2789 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: refined / Origin x: 10.8229 Å / Origin y: 9.267 Å / Origin z: 11.7333 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0324 Å2 | 0.0059 Å2 | 0.0027 Å2 | - | 0.0389 Å2 | -0.002 Å2 | - | - | 0.0153 Å2 |
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L | 0.7164 °2 | 0.2008 °2 | 0.2429 °2 | - | 1.0499 °2 | -0.088 °2 | - | - | 0.3475 °2 |
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S | 0.0114 Å ° | -0.0431 Å ° | -0.0411 Å ° | 0.1129 Å ° | -0.0235 Å ° | -0.0799 Å ° | -0.0211 Å ° | -0.036 Å ° | -0.0013 Å ° |
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Refinement TLS group | Selection details: chain A |
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