Software | Name | Version | Classification |
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PHENIX | 1.16_3549refinementPHENIX | 1.16_3549refinementHKL-2000 | | data reductionHKL-2000 | | data scalingPHENIX | | phasing | | | | | | |
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Refinement | Method to determine structure: MIR / Resolution: 2.6→32.77 Å / SU ML: 0.3349 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1705 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2633 | 1333 | 10 % |
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Rwork | 0.208 | 11991 | - |
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obs | 0.2134 | 13324 | 99.09 % |
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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: 61.27 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.6→32.77 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2960 | 0 | 0 | 37 | 2997 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0066 | 3027 | X-RAY DIFFRACTION | f_angle_d0.9716 | 4096 | X-RAY DIFFRACTION | f_chiral_restr0.0551 | 446 | X-RAY DIFFRACTION | f_plane_restr0.0075 | 523 | X-RAY DIFFRACTION | f_dihedral_angle_d14.3195 | 1451 | | | | | |
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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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2.6-2.7 | 0.3117 | 130 | 0.2407 | 1167 | X-RAY DIFFRACTION | 98.11 | 2.7-2.8 | 0.3257 | 131 | 0.2291 | 1177 | X-RAY DIFFRACTION | 100 | 2.8-2.93 | 0.3098 | 131 | 0.2366 | 1183 | X-RAY DIFFRACTION | 100 | 2.93-3.09 | 0.2875 | 133 | 0.2451 | 1197 | X-RAY DIFFRACTION | 99.92 | 3.09-3.28 | 0.3117 | 132 | 0.2288 | 1192 | X-RAY DIFFRACTION | 99.92 | 3.28-3.53 | 0.3006 | 132 | 0.2207 | 1186 | X-RAY DIFFRACTION | 100 | 3.53-3.89 | 0.2585 | 134 | 0.2121 | 1210 | X-RAY DIFFRACTION | 100 | 3.89-4.45 | 0.2281 | 137 | 0.1803 | 1221 | X-RAY DIFFRACTION | 100 | 4.45-5.6 | 0.2347 | 136 | 0.1777 | 1231 | X-RAY DIFFRACTION | 99.93 | 5.6-32.77 | 0.2458 | 137 | 0.2172 | 1227 | X-RAY DIFFRACTION | 93.62 |
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Refinement TLS params. | Method: refined / Origin x: 10.2863044184 Å / Origin y: 18.4122757955 Å / Origin z: 61.854107128 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.366972068841 Å2 | 0.0206818438957 Å2 | 0.0107392922735 Å2 | - | 0.267881061406 Å2 | 0.0384163878597 Å2 | - | - | 0.324773768727 Å2 |
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L | 1.86714580863 °2 | 0.28157550904 °2 | -0.947607629409 °2 | - | 1.55945596059 °2 | 0.00489689651222 °2 | - | - | 1.32684563083 °2 |
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S | -0.0333720175874 Å ° | -0.110081482318 Å ° | -0.0788285803543 Å ° | 0.198422583066 Å ° | 0.0181275936 Å ° | 0.112378862685 Å ° | 0.0152627289345 Å ° | 0.0497658559265 Å ° | 0.0261801861125 Å ° |
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Refinement TLS group | Selection details: ALL |
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