Software | Name | Version | Classification |
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PHENIX | (phenix.refine: 1.9_1692)refinementHKL-2000 | | data scalingPDB_EXTRACT | 3.15 | data extractionHKL-2000 | | data reductionPHENIX | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→49.679 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.98 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2338 | 1030 | 5.12 % | 0 |
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Rwork | 0.1894 | 19069 | - | - |
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obs | 0.1916 | 20099 | 97.93 % | - |
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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: 83.94 Å2 / Biso mean: 32.4137 Å2 / Biso min: 9.64 Å2 |
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Refinement step | Cycle: final / Resolution: 2.6→49.679 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2319 | 0 | 10 | 165 | 2494 |
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Biso mean | - | - | 34.63 | 35.83 | - |
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Num. residues | - | - | - | - | 301 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.013 | 2366 | X-RAY DIFFRACTION | f_angle_d1.239 | 3203 | X-RAY DIFFRACTION | f_chiral_restr0.08 | 366 | X-RAY DIFFRACTION | f_plane_restr0.005 | 422 | X-RAY DIFFRACTION | f_dihedral_angle_d14.025 | 889 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.5961-2.7329 | 0.3036 | 129 | 0.2278 | 2385 | 2514 | 88 | 2.7329-2.9041 | 0.2665 | 156 | 0.2256 | 2676 | 2832 | 99 | 2.9041-3.1283 | 0.2895 | 156 | 0.2153 | 2736 | 2892 | 100 | 3.1283-3.4431 | 0.2237 | 154 | 0.1919 | 2734 | 2888 | 100 | 3.4431-3.9411 | 0.2036 | 156 | 0.1713 | 2775 | 2931 | 100 | 3.9411-4.9647 | 0.194 | 139 | 0.1565 | 2817 | 2956 | 100 | 4.9647-49.6877 | 0.2394 | 140 | 0.195 | 2946 | 3086 | 99 |
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