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_289)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingRESOLVE | | phasing | | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→27.49 Å / SU ML: 0.21 / Isotropic thermal model: mixed / σ(F): 0 / Phase error: 19.34 / Stereochemistry target values: MLHL
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.198 | 1328 | 5.02 % |
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Rwork | 0.159 | - | - |
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obs | 0.161 | 26450 | 98.8 % |
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all | - | 26450 | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.816 Å2 / ksol: 0.32 e/Å3 |
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Displacement parameters | Biso mean: 36.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.1241 Å2 | -0 Å2 | -0 Å2 |
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2- | - | 0.1241 Å2 | 0 Å2 |
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3- | - | - | -0.2482 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.85→27.49 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2253 | 0 | 28 | 365 | 2646 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.011 | 2422 | X-RAY DIFFRACTION | f_angle_d1.264 | 3269 | X-RAY DIFFRACTION | f_dihedral_angle_d18.341 | 923 | X-RAY DIFFRACTION | f_chiral_restr0.088 | 369 | X-RAY DIFFRACTION | f_plane_restr0.005 | 423 | | | | | |
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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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1.85-1.9236 | 0.3087 | 117 | 0.2106 | 2744 | X-RAY DIFFRACTION | 99 | 1.9236-2.0111 | 0.2193 | 136 | 0.1834 | 2755 | X-RAY DIFFRACTION | 100 | 2.0111-2.1171 | 0.2041 | 147 | 0.1727 | 2755 | X-RAY DIFFRACTION | 100 | 2.1171-2.2497 | 0.1998 | 164 | 0.1646 | 2766 | X-RAY DIFFRACTION | 99 | 2.2497-2.4233 | 0.2457 | 151 | 0.1631 | 2757 | X-RAY DIFFRACTION | 99 | 2.4233-2.667 | 0.2259 | 155 | 0.1706 | 2796 | X-RAY DIFFRACTION | 100 | 2.667-3.0524 | 0.222 | 160 | 0.1636 | 2809 | X-RAY DIFFRACTION | 99 | 3.0524-3.8441 | 0.1735 | 162 | 0.1447 | 2830 | X-RAY DIFFRACTION | 99 | 3.8441-27.4957 | 0.1603 | 136 | 0.1466 | 2910 | X-RAY DIFFRACTION | 94 |
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Refinement TLS params. | Method: refined / Origin x: 4.7389 Å / Origin y: 29.9208 Å / Origin z: 80.3709 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1114 Å2 | 0.0174 Å2 | 0.0005 Å2 | - | 0.15 Å2 | 0.0012 Å2 | - | - | 0.1346 Å2 |
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L | 0.3792 °2 | -0.6193 °2 | 0.0203 °2 | - | 1.3478 °2 | 0.3145 °2 | - | - | 0.3163 °2 |
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S | 0.0129 Å ° | 0.1116 Å ° | 0.0203 Å ° | 0.0712 Å ° | -0.0454 Å ° | -0.0741 Å ° | 0.0151 Å ° | 0.0786 Å ° | 0.017 Å ° |
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Refinement TLS group | Selection details: chain A |
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