Software | Name | Version | Classification |
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PHENIX | (1.10.1_2155: ???)refinementXDS | | data reductionXSCALE | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2X1O Resolution: 1.8→38.9 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.58 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2216 | 1192 | 12 % |
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Rwork | 0.1868 | - | - |
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obs | 0.191 | 9930 | 99.88 % |
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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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Refinement step | Cycle: LAST / Resolution: 1.8→38.9 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 881 | 0 | 8 | 40 | 929 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.014 | 935 | X-RAY DIFFRACTION | f_angle_d1.414 | 1280 | X-RAY DIFFRACTION | f_dihedral_angle_d16.732 | 327 | X-RAY DIFFRACTION | f_chiral_restr0.084 | 138 | X-RAY DIFFRACTION | f_plane_restr0.006 | 167 | | | | | |
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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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1.8001-1.8722 | 0.3159 | 128 | 0.2921 | 940 | X-RAY DIFFRACTION | 99 | 1.8722-1.9574 | 0.2589 | 129 | 0.2378 | 947 | X-RAY DIFFRACTION | 100 | 1.9574-2.0606 | 0.2477 | 130 | 0.1988 | 954 | X-RAY DIFFRACTION | 100 | 2.0606-2.1897 | 0.2088 | 130 | 0.1798 | 949 | X-RAY DIFFRACTION | 100 | 2.1897-2.3588 | 0.2203 | 131 | 0.1725 | 962 | X-RAY DIFFRACTION | 100 | 2.3588-2.5961 | 0.2378 | 133 | 0.2015 | 973 | X-RAY DIFFRACTION | 100 | 2.5961-2.9716 | 0.2079 | 132 | 0.1874 | 974 | X-RAY DIFFRACTION | 100 | 2.9716-3.7435 | 0.2089 | 135 | 0.1669 | 984 | X-RAY DIFFRACTION | 100 | 3.7435-38.9089 | 0.2095 | 144 | 0.1774 | 1055 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: 14.6362 Å / Origin y: 1.6038 Å / Origin z: -3.8407 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.114 Å2 | 0.015 Å2 | -0.0137 Å2 | - | 0.1161 Å2 | -0.0075 Å2 | - | - | 0.1262 Å2 |
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L | 1.651 °2 | 0.1477 °2 | -0.8303 °2 | - | 2.6522 °2 | 0.957 °2 | - | - | 1.4611 °2 |
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S | 0.0355 Å ° | -0.0695 Å ° | -0.2097 Å ° | -0.1143 Å ° | 0.0458 Å ° | -0.0748 Å ° | 0.1041 Å ° | 0.0457 Å ° | 0.0369 Å ° |
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Refinement TLS group | Selection details: all |
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