Software | Name | Version | Classification |
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XDS | | data reductionPHENIX | (phenix.refine: 1.7_650)refinement Coot | | model buildingXSCALE | | data scaling | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BJ7 Resolution: 1.4→25.603 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.94 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2135 | 1589 | 5 % | Random |
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Rwork | 0.1963 | 30200 | - | - |
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obs | 0.1971 | 31789 | 96.93 % | - |
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.937 Å2 / ksol: 0.476 e/Å3 |
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Displacement parameters | Biso max: 55.47 Å2 / Biso mean: 14.0511 Å2 / Biso min: 4.56 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.2393 Å2 | -0 Å2 | 1.2922 Å2 |
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2- | - | 0.6536 Å2 | -0 Å2 |
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3- | - | - | 0.5858 Å2 |
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Refinement step | Cycle: final / Resolution: 1.4→25.603 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1229 | 0 | 0 | 67 | 1296 |
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Biso mean | - | - | - | 20.43 | - |
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Num. residues | - | - | - | - | 153 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 1276 | X-RAY DIFFRACTION | f_angle_d1.081 | 1732 | X-RAY DIFFRACTION | f_chiral_restr0.074 | 192 | X-RAY DIFFRACTION | f_plane_restr0.005 | 228 | X-RAY DIFFRACTION | f_dihedral_angle_d11.712 | 495 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.4-1.4452 | 0.3526 | 120 | 0.2854 | 2273 | 2393 | 82 | 1.4452-1.4968 | 0.2851 | 140 | 0.2533 | 2667 | 2807 | 95 | 1.4968-1.5568 | 0.2084 | 147 | 0.2148 | 2789 | 2936 | 99 | 1.5568-1.6276 | 0.2334 | 147 | 0.1915 | 2802 | 2949 | 100 | 1.6276-1.7134 | 0.2183 | 148 | 0.1899 | 2802 | 2950 | 99 | 1.7134-1.8207 | 0.1992 | 149 | 0.1762 | 2832 | 2981 | 99 | 1.8207-1.9612 | 0.2071 | 145 | 0.1817 | 2767 | 2912 | 99 | 1.9612-2.1585 | 0.1828 | 148 | 0.1755 | 2810 | 2958 | 98 | 2.1585-2.4706 | 0.1902 | 147 | 0.1745 | 2793 | 2940 | 98 | 2.4706-3.1119 | 0.2286 | 148 | 0.1959 | 2813 | 2961 | 99 | 3.1119-25.6076 | 0.2095 | 150 | 0.2087 | 2852 | 3002 | 97 |
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