Software | Name | Version | Classification |
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PHENIX | 1.11.1_2575refinementHKL-2000 | | data scalingPHASER | 2.7.16phasingPDB_EXTRACT | 3.24 | data extractionHKL-2000 | | data reduction | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+81 / Resolution: 2.901→46.506 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 33.34
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.3071 | 401 | 9.86 % |
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Rwork | 0.2524 | - | - |
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obs | 0.2575 | 4068 | 85.35 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 137.92 Å2 / Biso mean: 48.8336 Å2 / Biso min: 25.55 Å2 |
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Refinement step | Cycle: final / Resolution: 2.901→46.506 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 762 | 36 | 2 | 800 |
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Biso mean | - | - | 61.16 | 38.04 | - |
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Num. residues | - | - | - | - | 35 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.001 | 878 | X-RAY DIFFRACTION | f_angle_d0.292 | 1384 | X-RAY DIFFRACTION | f_chiral_restr0.019 | 175 | X-RAY DIFFRACTION | f_plane_restr0.002 | 37 | X-RAY DIFFRACTION | f_dihedral_angle_d12.365 | 417 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.9009-3.3205 | 0.305 | 136 | 0.2505 | 1208 | 1344 | 85 | 3.3205-4.1831 | 0.2705 | 135 | 0.2461 | 1212 | 1347 | 85 | 4.1831-46.512 | 0.3337 | 130 | 0.2572 | 1247 | 1377 | 86 |
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Refinement TLS params. | Method: refined / Origin x: 15.1918 Å / Origin y: 60.3891 Å / Origin z: 26.9675 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2789 Å2 | -0.0437 Å2 | 0.0145 Å2 | - | 0.453 Å2 | -0.0732 Å2 | - | - | 0.3376 Å2 |
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L | 2.874 °2 | 0.8669 °2 | -0.1169 °2 | - | 2.7529 °2 | -2.6408 °2 | - | - | 3.6548 °2 |
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S | 0.0255 Å ° | -0.6737 Å ° | 0.1916 Å ° | -0.0286 Å ° | -0.1524 Å ° | -0.0385 Å ° | 0.2144 Å ° | 0.3927 Å ° | 0.3963 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 | allA2 - 36 | 2 | X-RAY DIFFRACTION | 1 | allC1 | 3 | X-RAY DIFFRACTION | 1 | allC2 - 3 | 4 | X-RAY DIFFRACTION | 1 | allD1 | 5 | X-RAY DIFFRACTION | 1 | allE1 - 5 | 6 | X-RAY DIFFRACTION | 1 | allE6 | 7 | X-RAY DIFFRACTION | 1 | allF2 - 3 | 8 | X-RAY DIFFRACTION | 1 | allG1 | 9 | X-RAY DIFFRACTION | 1 | allG2 | 10 | X-RAY DIFFRACTION | 1 | allI1 | 11 | X-RAY DIFFRACTION | 1 | allI2 | | | | | | | | | | | | | | | | | | | | | | |
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