ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0019精密化 | SBC-Collect | | データ収集 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | SHELXD | | 位相決定 | MLPHARE | | 位相決定 | 直接法 | | 位相決定 | RESOLVE | | 位相決定 | HKL-3000 | | 位相決定 | |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 2.88→41.3 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 32.729 / SU ML: 0.29 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.345 / ESU R Free: 0.405 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.28278 | 891 | 5.1 % | RANDOM |
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Rwork | 0.21369 | - | - | - |
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all | 0.21703 | 16601 | - | - |
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obs | 0.21703 | 16601 | 98.46 % | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 77.618 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.28 Å2 | -0.14 Å2 | 0 Å2 |
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2- | - | -0.28 Å2 | 0 Å2 |
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3- | - | - | 0.42 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.88→41.3 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3930 | 0 | 0 | 0 | 3930 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.015 | 0.021 | 4011 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.654 | 1.953 | 5437 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.059 | 5 | 531 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg40.667 | 23.836 | 159 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg22.726 | 15 | 622 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg21.292 | 15 | 18 | X-RAY DIFFRACTION | r_chiral_restr0.117 | 0.2 | 628 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 3018 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.265 | 0.2 | 2029 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.321 | 0.2 | 2734 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.159 | 0.2 | 147 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.312 | 0.2 | 34 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.304 | 0.2 | 6 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.524 | 1.5 | 2685 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.952 | 2 | 4165 | X-RAY DIFFRACTION | r_scbond_it1.644 | 3 | 1446 | X-RAY DIFFRACTION | r_scangle_it2.616 | 4.5 | 1271 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.879→2.954 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.318 | 53 | - |
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Rwork | 0.26 | 1054 | - |
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obs | - | 1107 | 86.48 % |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 8.4026 | -0.1407 | 1.8062 | 1.0588 | -2.0851 | 4.3852 | -0.7859 | -0.1035 | 0.9516 | -0.2386 | 1.0512 | -0.6778 | -0.7658 | 0.1363 | -0.2653 | 0.2094 | -0.1352 | 0.0957 | 0.3447 | -0.3309 | 0.4827 | 65.105 | 78.853 | 26.333 | 2 | 9.1962 | 0.319 | 1.7538 | 3.6923 | -1.3533 | 3.4444 | -0.2336 | -1.7464 | -0.0339 | -0.0117 | 0.3237 | -0.1207 | -0.2219 | -0.4877 | -0.0901 | -0.5697 | 0.0525 | 0.0261 | 0.208 | 0.0231 | -0.37 | 70.015 | 49.407 | 28.647 | 3 | 7.4207 | 1.1214 | 1.8882 | 6.579 | 3.4325 | 4.9849 | -0.7233 | 0.6488 | 1.5124 | -0.1817 | 0.4618 | 0.7536 | -0.9865 | 0.058 | 0.2615 | 0.1722 | -0.1525 | -0.0329 | 0.3555 | 0.3766 | 0.3336 | 43.161 | 76.434 | 18.775 | 4 | 6.6177 | -1.3494 | 2.2913 | 4.9941 | -0.8915 | 3.6184 | -0.201 | 0.7415 | 0.1318 | 0.1287 | 0.1286 | 0.2988 | -0.0385 | -0.0133 | 0.0723 | -0.5916 | -0.0245 | 0.0503 | -0.0865 | 0.0148 | -0.4143 | 39.482 | 49.137 | 29.047 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA71 - 169 | 4 - 102 | 2 | X-RAY DIFFRACTION | 1 | AA302 - 321 | 235 - 254 | 3 | X-RAY DIFFRACTION | 2 | AA170 - 301 | 103 - 234 | 4 | X-RAY DIFFRACTION | 2 | AA328 - 340 | 261 - 273 | 5 | X-RAY DIFFRACTION | 3 | BB71 - 169 | 4 - 102 | 6 | X-RAY DIFFRACTION | 3 | BB302 - 324 | 235 - 257 | 7 | X-RAY DIFFRACTION | 4 | BB170 - 301 | 103 - 234 | 8 | X-RAY DIFFRACTION | 4 | BB326 - 342 | 259 - 275 | | | | | | | | | | | | | | | | |
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