ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | SHELXD | | 位相決定 | MLPHARE | | 位相決定 | 直接法 | | モデル構築 | RESOLVE | | モデル構築 | HKL-3000 | | 位相決定 | REFMAC | 5.5.0102精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | 直接法 | | 位相決定 | RESOLVE | | 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: 3.2→44.9 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.935 / SU B: 43.657 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / 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 | 0.26112 | 483 | 4.8 % | RANDOM |
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Rwork | 0.22306 | - | - | - |
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all | 0.22498 | 9531 | - | - |
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obs | 0.22498 | 9531 | 99.7 % | - |
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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: 1.4 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 48.216 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.24 Å2 | 0.62 Å2 | 0 Å2 |
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2- | - | 1.24 Å2 | 0 Å2 |
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3- | - | - | -1.86 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 3.2→44.9 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2372 | 0 | 24 | 0 | 2396 |
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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_d0.017 | 0.022 | 2441 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.777 | 1.958 | 3281 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.023 | 5 | 296 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.434 | 24.144 | 111 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg24.535 | 15 | 449 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg20.035 | 15 | 12 | X-RAY DIFFRACTION | r_chiral_restr0.117 | 0.2 | 364 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 1793 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | 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_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | 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_it0.542 | 1.5 | 1472 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.056 | 2 | 2357 | X-RAY DIFFRACTION | r_scbond_it1.748 | 3 | 969 | X-RAY DIFFRACTION | r_scangle_it3.04 | 4.5 | 924 | 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: 3.198→3.281 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.331 | 34 | - |
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Rwork | 0.349 | 686 | - |
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obs | - | 720 | 99.45 % |
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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 | 15.6924 | -3.2817 | 8.2339 | 5.6517 | -5.855 | 11.7122 | 0.1845 | -0.8979 | -0.3908 | 0.1023 | 0.1787 | 0.8098 | 0.2791 | -0.7914 | -0.3632 | 0.2549 | -0.0655 | -0.0375 | 0.382 | 0.0936 | 0.8635 | -10.755 | 59.099 | 44.25 | 2 | 5.7009 | -0.2224 | 4.2394 | 2.0361 | -0.8005 | 13.6814 | -0.193 | -0.2243 | 0.3866 | -0.0453 | 0.1952 | 0.272 | -0.2195 | -0.0459 | -0.0021 | 0.1771 | -0.007 | 0.0115 | -0.0055 | -0.0143 | 0.8185 | 9.798 | 54.963 | 57.128 | 3 | 6.6161 | 2.6 | 4.1104 | 4.0422 | -1.1501 | 13.4854 | 0.2075 | 1.0534 | -0.5194 | -0.5143 | -0.1587 | 0.2311 | 0.1291 | 0.605 | -0.0488 | 0.6316 | 0.1878 | -0.1109 | 0.7499 | -0.0281 | 1.0279 | 15.931 | 49.848 | 22.284 | 4 | 12.4336 | -2.6355 | 0.9165 | 2.5392 | -1.2363 | 5.4774 | 0.369 | 0.5347 | 0.4022 | -0.7525 | -0.202 | -0.3498 | -0.4733 | -0.0208 | -0.167 | 0.4867 | 0.0486 | 0.0742 | 0.1614 | 0.0228 | 0.7818 | 25.748 | 52.106 | 44.975 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A5 - 62 | 2 | X-RAY DIFFRACTION | 2 | A63 - 153 | 3 | X-RAY DIFFRACTION | 3 | B5 - 62 | 4 | X-RAY DIFFRACTION | 4 | B63 - 153 | | | | |
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