Software | Name | Version | Classification |
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PHENIX | 1.11.1_2575refinementAimless | 0.5.32data scalingPDB_EXTRACT | 3.24 | data extractionXDS | | data reductionPHENIX | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.695→31.912 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.27 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.177 | 1264 | 4.85 % |
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Rwork | 0.1516 | 24791 | - |
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obs | 0.1529 | 26055 | 97.54 % |
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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: 107.54 Å2 / Biso mean: 23.2248 Å2 / Biso min: 8.51 Å2 |
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Refinement step | Cycle: final / Resolution: 1.695→31.912 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2049 | 0 | 28 | 138 | 2215 |
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Biso mean | - | - | 21.93 | 27.03 | - |
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Num. residues | - | - | - | - | 257 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.01 | 2131 | X-RAY DIFFRACTION | f_angle_d1.091 | 2891 | X-RAY DIFFRACTION | f_chiral_restr0.06 | 300 | X-RAY DIFFRACTION | f_plane_restr0.007 | 376 | X-RAY DIFFRACTION | f_dihedral_angle_d13.343 | 1251 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.6946-1.7625 | 0.2516 | 139 | 0.1964 | 2701 | 2840 | 96 | 1.7625-1.8427 | 0.2201 | 136 | 0.1791 | 2725 | 2861 | 97 | 1.8427-1.9398 | 0.2024 | 121 | 0.1655 | 2713 | 2834 | 97 | 1.9398-2.0613 | 0.1878 | 153 | 0.1531 | 2713 | 2866 | 98 | 2.0613-2.2204 | 0.1794 | 133 | 0.1422 | 2745 | 2878 | 97 | 2.2204-2.4438 | 0.2083 | 155 | 0.1453 | 2742 | 2897 | 98 | 2.4438-2.7973 | 0.2094 | 139 | 0.1531 | 2790 | 2929 | 98 | 2.7973-3.5235 | 0.1555 | 135 | 0.1456 | 2797 | 2932 | 98 | 3.5235-31.9178 | 0.1406 | 153 | 0.1457 | 2865 | 3018 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -30.5533 Å / Origin y: -1.8585 Å / Origin z: 15.8622 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0447 Å2 | 0.0008 Å2 | 0.0005 Å2 | - | 0.0425 Å2 | -0.001 Å2 | - | - | 0.0461 Å2 |
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L | 0.275 °2 | -0.0379 °2 | 0.0421 °2 | - | 0.1882 °2 | -0.034 °2 | - | - | 0.2015 °2 |
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S | -0.0148 Å ° | -0.0283 Å ° | 0.0085 Å ° | -0.0303 Å ° | 0.0085 Å ° | 0.0068 Å ° | 0.0044 Å ° | 0.0011 Å ° | -0 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 | allA4 - 261 | 2 | X-RAY DIFFRACTION | 1 | allB262 | 3 | X-RAY DIFFRACTION | 1 | allD3 - 143 | 4 | X-RAY DIFFRACTION | 1 | allC1 | 5 | X-RAY DIFFRACTION | 1 | allE400 | | | | | | | | | | |
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