Software | Name | Version | Classification |
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XDS | | data reductionAimless | | data scalingPHENIX | 1.11.1_2575refinementPDB_EXTRACT | 3.27 | data extractionPHENIX | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DDC Resolution: 2.159→47.996 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.98 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2517 | 1580 | 4.63 % |
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Rwork | 0.2073 | 32514 | - |
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obs | 0.2093 | 34094 | 99.96 % |
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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: 85.81 Å2 / Biso mean: 41.6412 Å2 / Biso min: 19.64 Å2 |
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Refinement step | Cycle: final / Resolution: 2.159→47.996 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3614 | 0 | 8 | 95 | 3717 |
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Biso mean | - | - | 43.37 | 37.59 | - |
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Num. residues | - | - | - | - | 457 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 3698 | X-RAY DIFFRACTION | f_angle_d0.828 | 5007 | X-RAY DIFFRACTION | f_chiral_restr0.047 | 559 | X-RAY DIFFRACTION | f_plane_restr0.005 | 639 | X-RAY DIFFRACTION | f_dihedral_angle_d9.788 | 2198 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 % Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork |
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2.159-2.2287 | 0.325 | 151 | 0.2503 | 2881 | 2.2287-2.3083 | 0.3106 | 129 | 0.2438 | 2908 | 2.236-4.8001 | 0.2378 | 129 | 0.1916 | 3209 | 2.3083-2.4008 | 0.2653 | 186 | 0.2321 | 2858 | 2.4008-2.51 | 0.3387 | 143 | 0.2348 | 2915 | 2.51-2.6423 | 0.2842 | 136 | 0.2287 | 2918 | 2.6423-2.8079 | 0.3057 | 174 | 0.2403 | 2906 | 2.8079-3.0246 | 0.2416 | 130 | 0.2171 | 2946 | 3.0246-3.329 | 0.2402 | 118 | 0.2101 | 2981 | 3.329-3.8105 | 0.2225 | 139 | 0.1986 | 2989 | 3.8105-4.8001 | 0.2224 | 145 | 0.1842 | 3003 |
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