Software | Name | Version | Classification |
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MAR345dtb | | data collectionMOLREP | | phasingPHENIX | (phenix.refine)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.513→22.042 Å / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: TWIN_LSQ_F
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2479 | 1115 | 5.11 % |
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Rwork | 0.2183 | - | - |
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obs | 0.2198 | 21834 | 99.68 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.795 Å2 / ksol: 0.418 e/Å3 |
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Displacement parameters | Biso mean: 22.781 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.729 Å2 | -0 Å2 | 0 Å2 |
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2- | - | -2.729 Å2 | -0 Å2 |
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3- | - | - | 1.37 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.513→22.042 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1252 | 0 | 6 | 96 | 1354 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.012 | 1281 | X-RAY DIFFRACTION | f_angle_d1.285 | 1722 | X-RAY DIFFRACTION | f_dihedral_angle_d15.164 | 458 | X-RAY DIFFRACTION | f_chiral_restr0.338 | 210 | X-RAY DIFFRACTION | f_plane_restr0.006 | 217 | | | | | |
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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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1.5126-1.5614 | 0.3314 | 93 | 0.2939 | 1862 | X-RAY DIFFRACTION | 98 | 1.5614-1.6172 | 0.3285 | 90 | 0.283 | 1880 | X-RAY DIFFRACTION | 98 | 1.6172-1.6819 | 0.2968 | 107 | 0.2831 | 1851 | X-RAY DIFFRACTION | 98 | 1.6819-1.7584 | 0.2763 | 100 | 0.2673 | 1884 | X-RAY DIFFRACTION | 98 | 1.7584-1.8511 | 0.3108 | 100 | 0.2641 | 1872 | X-RAY DIFFRACTION | 98 | 1.8511-1.967 | 0.3035 | 95 | 0.251 | 1881 | X-RAY DIFFRACTION | 98 | 1.967-2.1187 | 0.2349 | 106 | 0.2331 | 1889 | X-RAY DIFFRACTION | 98 | 2.1187-2.3318 | 0.2349 | 111 | 0.223 | 1865 | X-RAY DIFFRACTION | 98 | 2.3318-2.6687 | 0.2465 | 97 | 0.2103 | 1905 | X-RAY DIFFRACTION | 98 | 2.6687-3.3603 | 0.2475 | 107 | 0.2002 | 1906 | X-RAY DIFFRACTION | 98 | 3.3603-22.0442 | 0.2108 | 109 | 0.1795 | 1924 | X-RAY DIFFRACTION | 98 |
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Refinement TLS params. | Method: refined / Origin x: 20.9221 Å / Origin y: 8.0754 Å / Origin z: 10.6194 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1213 Å2 | 0.0302 Å2 | -0.0003 Å2 | - | 0.1211 Å2 | 0.0061 Å2 | - | - | 0.0866 Å2 |
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L | 0.1093 °2 | 0.0273 °2 | -0.0544 °2 | - | 0.1706 °2 | -0.0394 °2 | - | - | 0.8033 °2 |
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S | -0.0591 Å ° | 0.0044 Å ° | 0.0153 Å ° | 0.012 Å ° | 0.0767 Å ° | 0.0353 Å ° | -0.1778 Å ° | -0.134 Å ° | -0.0118 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 | allA1 - 87 | 2 | X-RAY DIFFRACTION | 1 | allB1 - 87 | 3 | X-RAY DIFFRACTION | 1 | allC1 - 6 | 4 | X-RAY DIFFRACTION | 1 | allS1 - 110 | | | | | | | | |
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