Software | Name | Version | Classification |
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DENZO | | data collectionHKL-2000 | | data scalingPHASES | | phasingRESOLVE | 2.15 | model buildingPHENIX | dev_1819refinementPDB_EXTRACT | 3.15 | data extraction | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2→24.682 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 23.23 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2332 | 833 | 5 % | Random selection |
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Rwork | 0.1853 | 15832 | - | - |
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obs | 0.1877 | 16665 | 98.82 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso max: 91.9 Å2 / Biso mean: 28.1482 Å2 / Biso min: 7.66 Å2 |
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Refinement step | Cycle: final / Resolution: 2→24.682 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1798 | 0 | 0 | 171 | 1969 |
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Biso mean | - | - | - | 36.06 | - |
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Num. residues | - | - | - | - | 233 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 1818 | X-RAY DIFFRACTION | f_angle_d0.728 | 2456 | X-RAY DIFFRACTION | f_chiral_restr0.025 | 296 | X-RAY DIFFRACTION | f_plane_restr0.004 | 320 | X-RAY DIFFRACTION | f_dihedral_angle_d14.619 | 678 | | | | | |
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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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1.9953-2.1203 | 0.2924 | 131 | 0.2163 | 2496 | X-RAY DIFFRACTION | 95 | 2.1203-2.2839 | 0.2722 | 137 | 0.2101 | 2593 | X-RAY DIFFRACTION | 99 | 2.2839-2.5135 | 0.2612 | 138 | 0.2148 | 2628 | X-RAY DIFFRACTION | 99 | 2.5135-2.8767 | 0.2446 | 140 | 0.2091 | 2657 | X-RAY DIFFRACTION | 100 | 2.8767-3.6226 | 0.2433 | 141 | 0.1803 | 2676 | X-RAY DIFFRACTION | 100 | 3.6226-10 | 0.182 | 146 | 0.1531 | 2782 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: 13.5412 Å / Origin y: 42.524 Å / Origin z: 26.3433 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1054 Å2 | 0.003 Å2 | 0.0213 Å2 | - | 0.0598 Å2 | -0.0103 Å2 | - | - | 0.1435 Å2 |
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L | 2.4095 °2 | 0.382 °2 | 0.3612 °2 | - | 2.4567 °2 | 0.1667 °2 | - | - | 1.3259 °2 |
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S | -0.0043 Å ° | 0.0446 Å ° | -0.0574 Å ° | -0.2268 Å ° | -0.0448 Å ° | -0.2214 Å ° | -0.0313 Å ° | -0.0526 Å ° | 0.0386 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 - 118 | 2 | X-RAY DIFFRACTION | 1 | allB4 - 119 | 3 | X-RAY DIFFRACTION | 1 | allA201 - 298 | 4 | X-RAY DIFFRACTION | 1 | allB201 - 273 | | | | | | | | |
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