Software | Name | Version | Classification |
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SBC-Collect | | data collectionSHELXD | | phasingMLPHARE | | phasingDM | | model buildingARP | | model buildingWARP | | model buildingHKL-3000 | | phasingPHENIX | (phenix.refine: 1.5_2)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingDM | | phasing | | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.39→24.656 Å / SU ML: 0.18 / σ(F): 0.04 / σ(I): 0 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.211 | 3268 | 5.05 % | random |
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Rwork | 0.1873 | - | - | - |
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all | 0.1885 | 64679 | - | - |
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obs | 0.1885 | 64679 | 91.53 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.671 Å2 / ksol: 0.392 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.1311 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 0.0545 Å2 | 0 Å2 |
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3- | - | - | -3.1856 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.39→24.656 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2368 | 0 | 30 | 401 | 2799 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 2514 | X-RAY DIFFRACTION | f_angle_d1.092 | 3423 | X-RAY DIFFRACTION | f_dihedral_angle_d17.335 | 944 | X-RAY DIFFRACTION | f_chiral_restr0.073 | 369 | X-RAY DIFFRACTION | f_plane_restr0.005 | 455 | | | | | |
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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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1.3896-1.4392 | 0.3033 | 287 | 0.2727 | 5234 | X-RAY DIFFRACTION | 79 | 1.4392-1.4969 | 0.2525 | 300 | 0.2241 | 5717 | X-RAY DIFFRACTION | 86 | 1.4969-1.565 | 0.2422 | 308 | 0.2005 | 5870 | X-RAY DIFFRACTION | 89 | 1.565-1.6475 | 0.221 | 346 | 0.1775 | 6096 | X-RAY DIFFRACTION | 92 | 1.6475-1.7506 | 0.192 | 353 | 0.1712 | 6166 | X-RAY DIFFRACTION | 93 | 1.7506-1.8858 | 0.1905 | 322 | 0.1739 | 6331 | X-RAY DIFFRACTION | 95 | 1.8858-2.0755 | 0.2064 | 358 | 0.1725 | 6465 | X-RAY DIFFRACTION | 97 | 2.0755-2.3756 | 0.1914 | 322 | 0.1635 | 6665 | X-RAY DIFFRACTION | 99 | 2.3756-2.9921 | 0.2012 | 353 | 0.1806 | 6728 | X-RAY DIFFRACTION | 99 | 2.9921-24.6599 | 0.2073 | 319 | 0.1903 | 6139 | X-RAY DIFFRACTION | 87 |
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Refinement TLS params. | Method: refined / Origin x: 21.6357 Å / Origin y: 20.8609 Å / Origin z: 18.4435 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.093 Å2 | -0.0005 Å2 | -0.0031 Å2 | - | 0.0995 Å2 | 0.0012 Å2 | - | - | 0.1087 Å2 |
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L | 0.427 °2 | -0.0707 °2 | -0.0804 °2 | - | 0.3808 °2 | 0.0635 °2 | - | - | 1.1215 °2 |
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S | 0.008 Å ° | -0.0132 Å ° | -0.0168 Å ° | 0.0234 Å ° | 0.0072 Å ° | 0.0251 Å ° | 0.058 Å ° | -0.0822 Å ° | -0.0117 Å ° |
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Refinement TLS group | Selection details: chain A |
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