Software | Name | Version | Classification |
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PHENIX | 1.19.2_4158refinement Coot | 0.9.5model buildingxia2 | | data reductionDIALS | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8EYU Resolution: 2.1→47.3 Å / SU ML: 0.2267 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3495 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: For the most disordered regions, the modeled nucleotides were refined with occupancy = 0. The list of nucleotides: chain A - C2, G48, C49, chain B - G3, C4, G6, U9, G46, C47, G48, and C49.
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2202 | 1544 | 9.38 % |
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Rwork | 0.1798 | 14921 | - |
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obs | 0.1832 | 16467 | 99.55 % |
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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 mean: 65.6 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.1→47.3 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 2017 | 45 | 113 | 2175 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0061 | 2354 | X-RAY DIFFRACTION | f_angle_d1.1495 | 3672 | X-RAY DIFFRACTION | f_chiral_restr0.0596 | 471 | X-RAY DIFFRACTION | f_plane_restr0.009 | 101 | X-RAY DIFFRACTION | f_dihedral_angle_d19.9696 | 1139 | | | | | |
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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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2.1-2.17 | 0.2891 | 138 | 0.2285 | 1320 | X-RAY DIFFRACTION | 98.58 | 2.17-2.25 | 0.3158 | 131 | 0.2277 | 1341 | X-RAY DIFFRACTION | 99.93 | 2.25-2.34 | 0.2465 | 131 | 0.2015 | 1364 | X-RAY DIFFRACTION | 99.47 | 2.34-2.44 | 0.262 | 127 | 0.2061 | 1374 | X-RAY DIFFRACTION | 99.6 | 2.44-2.57 | 0.2561 | 135 | 0.1987 | 1343 | X-RAY DIFFRACTION | 99.86 | 2.57-2.73 | 0.2309 | 101 | 0.2175 | 1386 | X-RAY DIFFRACTION | 99.13 | 2.73-2.94 | 0.2645 | 149 | 0.2154 | 1365 | X-RAY DIFFRACTION | 99.87 | 2.94-3.24 | 0.1949 | 150 | 0.181 | 1346 | X-RAY DIFFRACTION | 99.6 | 3.24-3.71 | 0.2132 | 166 | 0.1606 | 1337 | X-RAY DIFFRACTION | 99.54 | 3.71-4.67 | 0.1911 | 157 | 0.136 | 1346 | X-RAY DIFFRACTION | 100 | 4.67-47.3 | 0.1947 | 159 | 0.166 | 1399 | X-RAY DIFFRACTION | 99.43 |
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Refinement TLS params. | Method: refined / Origin x: 5.22297827637 Å / Origin y: -4.7482821577 Å / Origin z: 4.38437224595 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.224475136198 Å2 | 0.0110264610086 Å2 | -0.166652358382 Å2 | - | 0.093764266522 Å2 | -0.0205220435044 Å2 | - | - | 0.459549625923 Å2 |
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L | 3.2778533518 °2 | 0.175257730896 °2 | -0.164321080835 °2 | - | 1.47504104428 °2 | -0.590211145615 °2 | - | - | 1.65964335249 °2 |
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S | 0.0264922297212 Å ° | -0.151533044699 Å ° | -0.0658077880391 Å ° | 0.132731284834 Å ° | 0.0395143925426 Å ° | -0.031778988659 Å ° | 0.0592665354267 Å ° | 0.155914339492 Å ° | -0.0837848697745 Å ° |
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Refinement TLS group | Selection details: all |
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