ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0005精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | SHELXD | | 位相決定 | SOLVE | | 位相決定 | RESOLVE | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.9→60.08 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.175 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.135 / 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 | 0.20807 | 1384 | 5 % | RANDOM |
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Rwork | 0.18566 | - | - | - |
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all | 0.18682 | 27528 | - | - |
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obs | 0.18681 | 26144 | 98 % | - |
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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 |
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原子変位パラメータ | Biso mean: 19.57 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.75 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 1.25 Å2 | 0 Å2 |
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3- | - | - | -0.5 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→60.08 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2619 | 0 | 0 | 266 | 2885 |
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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_d0.01 | 0.021 | 2710 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.17 | 1.939 | 3688 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.633 | 5 | 346 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.186 | 23.134 | 134 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.473 | 15 | 416 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg11.933 | 15 | 28 | X-RAY DIFFRACTION | r_chiral_restr0.082 | 0.2 | 396 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 2148 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.184 | 0.2 | 1206 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.301 | 0.2 | 1878 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.294 | 0.2 | 233 | 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_it0.729 | 1.5 | 1763 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.175 | 2 | 2707 | X-RAY DIFFRACTION | r_scbond_it1.953 | 3 | 1109 | X-RAY DIFFRACTION | r_scangle_it2.854 | 4.5 | 981 | 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: 1.9→1.949 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.239 | 107 | - |
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Rwork | 0.22 | 1913 | - |
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obs | - | - | 99.36 % |
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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 | 0.8183 | -0.2494 | -0.0125 | 0.7315 | -0.2794 | 1.2929 | -0.0119 | 0.14 | 0.0513 | -0.0948 | 0.0501 | 0.0089 | 0.0877 | -0.0197 | -0.0383 | -0.0517 | -0.0479 | -0.0052 | 0.0125 | -0.0081 | -0.0668 | 17.468 | 63.752 | 16.821 | 2 | 1.3158 | 0.0605 | -0.0885 | 1.0403 | -0.1196 | 0.6171 | 0.0135 | 0.0495 | 0.1117 | 0.0744 | -0.0296 | -0.0545 | -0.0203 | -0.0662 | 0.0162 | -0.0606 | 0.0107 | -0.014 | -0.0401 | 0.0072 | -0.039 | 33.923 | 73.787 | 36.134 |
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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 | AA4 - 172 | 4 - 172 | 2 | X-RAY DIFFRACTION | 2 | BB4 - 172 | 4 - 172 | | | | |
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