Software | Name | Version | Classification |
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Aimless | 0.5.9data scalingPHENIX | 1.8.4_1496refinementPDB_EXTRACT | 3.15 | data extractionXSCALE | | data scalingAutoSol | | phasing | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.933→29.475 Å / FOM work R set: 0.7379 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.54 / Stereochemistry target values: MLHL
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.289 | 1667 | 9.98 % |
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Rwork | 0.2098 | 15040 | - |
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obs | 0.2178 | 16707 | 98.91 % |
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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: 126.93 Å2 / Biso mean: 57.48 Å2 / Biso min: 20 Å2 |
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Refinement step | Cycle: final / Resolution: 2.933→29.475 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4663 | 0 | 63 | 12 | 4738 |
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Biso mean | - | - | 77.21 | 52.94 | - |
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Num. residues | - | - | - | - | 626 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 4794 | X-RAY DIFFRACTION | f_angle_d1.301 | 6500 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 748 | X-RAY DIFFRACTION | f_plane_restr0.006 | 846 | X-RAY DIFFRACTION | f_dihedral_angle_d14.443 | 1677 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.9326-3.0188 | 0.3678 | 126 | 0.2591 | 1189 | 1315 | 96 | 3.0188-3.1161 | 0.3417 | 136 | 0.226 | 1210 | 1346 | 97 | 3.1161-3.2273 | 0.3356 | 131 | 0.2159 | 1214 | 1345 | 98 | 3.2273-3.3564 | 0.3069 | 138 | 0.207 | 1231 | 1369 | 99 | 3.3564-3.5089 | 0.3169 | 138 | 0.2065 | 1232 | 1370 | 99 | 3.5089-3.6936 | 0.3013 | 134 | 0.1949 | 1241 | 1375 | 99 | 3.6936-3.9245 | 0.2626 | 141 | 0.1933 | 1258 | 1399 | 99 | 3.9245-4.2267 | 0.2645 | 130 | 0.1923 | 1277 | 1407 | 100 | 4.2267-4.6506 | 0.2778 | 145 | 0.181 | 1257 | 1402 | 100 | 4.6506-5.3201 | 0.2729 | 144 | 0.2057 | 1272 | 1416 | 100 | 5.3201-6.6898 | 0.2824 | 143 | 0.2454 | 1290 | 1433 | 100 | 6.6898-29.4768 | 0.2862 | 161 | 0.2221 | 1369 | 1530 | 100 |
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