Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE)refinementMOSFLM | | data reductionSCALA | | data scalingSOLVE | | phasing | | | | |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.229→34.872 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 16.14 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1782 | 2586 | 5 % |
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Rwork | 0.1453 | - | - |
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obs | 0.147 | 51279 | 99.32 % |
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.657 Å2 / ksol: 0.375 e/Å3 |
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Displacement parameters | Biso mean: 18.91 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 5.0148 Å2 | 0 Å2 | 0.5039 Å2 |
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2- | - | -0.6054 Å2 | 0 Å2 |
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3- | - | - | -4.4094 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.229→34.872 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1395 | 0 | 12 | 268 | 1675 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.014 | 1465 | X-RAY DIFFRACTION | f_angle_d1.559 | 1996 | X-RAY DIFFRACTION | f_dihedral_angle_d14.225 | 557 | X-RAY DIFFRACTION | f_chiral_restr0.107 | 207 | X-RAY DIFFRACTION | f_plane_restr0.008 | 263 | | | | | |
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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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1.2291-1.273 | 0.3101 | 227 | 0.2724 | 4763 | X-RAY DIFFRACTION | 98 | 1.273-1.324 | 0.2364 | 251 | 0.2032 | 4827 | X-RAY DIFFRACTION | 99 | 1.324-1.3843 | 0.2053 | 269 | 0.1645 | 4832 | X-RAY DIFFRACTION | 99 | 1.3843-1.4572 | 0.2015 | 266 | 0.1402 | 4809 | X-RAY DIFFRACTION | 99 | 1.4572-1.5485 | 0.1484 | 280 | 0.1115 | 4820 | X-RAY DIFFRACTION | 99 | 1.5485-1.6681 | 0.1641 | 236 | 0.1097 | 4900 | X-RAY DIFFRACTION | 100 | 1.6681-1.836 | 0.1684 | 252 | 0.1156 | 4875 | X-RAY DIFFRACTION | 100 | 1.836-2.1016 | 0.1503 | 261 | 0.1261 | 4915 | X-RAY DIFFRACTION | 100 | 2.1016-2.6477 | 0.182 | 261 | 0.1423 | 4949 | X-RAY DIFFRACTION | 100 | 2.6477-34.8856 | 0.1776 | 283 | 0.1557 | 5003 | X-RAY DIFFRACTION | 100 |
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