Software | Name | Version | Classification |
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HKL-2000 | | data collectionSOLVE | | phasingPHENIX | (phenix.refine)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→28.566 Å / SU ML: 0.31 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 27.53 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2726 | 687 | 5.22 % | RANDOM |
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Rwork | 0.2046 | - | - | - |
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all | 0.2302 | 14029 | - | - |
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obs | 0.2081 | 13152 | 97.08 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.047 Å2 / ksol: 0.407 e/Å3 |
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Displacement parameters | Biso mean: 42.33 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 18.0206 Å2 | 0 Å2 | -0 Å2 |
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2- | - | -1.676 Å2 | 0 Å2 |
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3- | - | - | -16.3445 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.038 Å | 0.03 Å |
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Luzzati d res low | - | 6 Å |
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Luzzati sigma a | 0.5 Å | 0.2 Å |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.566 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1903 | 0 | 0 | 128 | 2031 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 1964 | X-RAY DIFFRACTION | f_angle_d1.27 | 2660 | X-RAY DIFFRACTION | f_dihedral_angle_d18.757 | 753 | X-RAY DIFFRACTION | f_chiral_restr0.088 | 281 | X-RAY DIFFRACTION | f_plane_restr0.008 | 340 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Rfactor Rfree error | Num. reflection obs | % reflection obs (%) |
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2.2-2.3698 | 0.3426 | 143 | 0.2115 | 2479 | 0.01 | 2566 | 98 | 2.3698-2.6081 | 0.2894 | 144 | 0.2012 | 2476 | 0.01 | 2673 | 99 | 2.6081-2.9852 | 0.3105 | 144 | 0.1819 | 2527 | 0.011 | 2671 | 99 | 2.9852-3.7597 | 0.2346 | 136 | 0.1712 | 2537 | 0.012 | 2620 | 99 | 3.7597-28.5684 | 0.2611 | 120 | 0.2337 | 2446 | 0.012 | 2622 | 90 |
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Refinement TLS params. | Method: refined / Origin x: 16.1582 Å / Origin y: -2.6088 Å / Origin z: -11.6143 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1267 Å2 | 0.0324 Å2 | 0.0042 Å2 | - | 0.1266 Å2 | 0.0254 Å2 | - | - | 0.1484 Å2 |
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L | 0.6363 °2 | -0.0295 °2 | -0.0518 °2 | - | 0.7843 °2 | 0.3696 °2 | - | - | 2.1272 °2 |
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S | -0.0279 Å ° | -0.0355 Å ° | -0.0537 Å ° | 0.2001 Å ° | 0.0879 Å ° | -0.0059 Å ° | 0.156 Å ° | 0.2024 Å ° | -0.0002 Å ° |
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Refinement TLS group | Selection details: all |
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