ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | SHARP | | 位相決定 | | 直接法 | 5 | 位相決定 | | REFMAC | refmac_5.5.0102精密化 | | PDB_EXTRACT | 3.005 | データ抽出 | | JDirector | | データ収集 | | HKL-2000 | | データ削減 | | HKL-2000 | | データスケーリング | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.451→19.834 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.197 / ESU R: 0.382 / ESU R Free: 0.245 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 |
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Rfree | 0.237 | 752 | 5.011 % |
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Rwork | 0.2089 | - | - |
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obs | - | 15007 | 99.036 % |
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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: BABINET MODEL PLUS MASK |
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原子変位パラメータ | Biso mean: 45.422 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.065 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.073 Å2 | 0 Å2 |
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3- | - | - | 0.008 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.451→19.834 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2402 | 0 | 0 | 28 | 2430 |
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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 | 0.022 | 2458 | X-RAY DIFFRACTION | r_angle_refined_deg1.528 | 1.932 | 3312 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.299 | 5 | 297 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.567 | 25.338 | 133 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg18.767 | 15 | 417 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg8.54 | 15 | 6 | X-RAY DIFFRACTION | r_chiral_restr0.107 | 0.2 | 340 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 1911 | X-RAY DIFFRACTION | r_nbd_refined0.199 | 0.2 | 863 | X-RAY DIFFRACTION | r_nbtor_refined0.305 | 0.2 | 1646 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.132 | 0.2 | 64 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.174 | 0.2 | 48 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.092 | 0.2 | 3 | X-RAY DIFFRACTION | r_mcbond_it0.762 | 1.5 | 1474 | X-RAY DIFFRACTION | r_mcangle_it1.531 | 2 | 2348 | X-RAY DIFFRACTION | r_scbond_it2.368 | 3 | 984 | X-RAY DIFFRACTION | r_scangle_it3.99 | 4.5 | 964 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.451-2.513 | 0.381 | 47 | 0.238 | 1034 | 1098 | 98.452 | 2.513-2.581 | 0.266 | 40 | 0.226 | 998 | 1051 | 98.763 | 2.581-2.654 | 0.301 | 64 | 0.239 | 956 | 1033 | 98.742 | 2.654-2.735 | 0.316 | 43 | 0.246 | 951 | 1004 | 99.004 | 2.735-2.823 | 0.302 | 45 | 0.257 | 901 | 967 | 97.828 | 2.823-2.919 | 0.32 | 53 | 0.236 | 879 | 949 | 98.209 | 2.919-3.027 | 0.327 | 46 | 0.234 | 868 | 921 | 99.24 | 3.027-3.148 | 0.305 | 42 | 0.214 | 848 | 892 | 99.776 | 3.148-3.284 | 0.258 | 35 | 0.224 | 801 | 837 | 99.881 | 3.284-3.439 | 0.294 | 47 | 0.216 | 762 | 812 | 99.631 | 3.439-3.62 | 0.225 | 38 | 0.201 | 738 | 780 | 99.487 | 3.62-3.831 | 0.226 | 32 | 0.215 | 723 | 755 | 100 | 3.831-4.085 | 0.219 | 30 | 0.196 | 642 | 684 | 98.246 | 4.085-4.397 | 0.167 | 38 | 0.177 | 613 | 659 | 98.786 | 4.397-4.793 | 0.153 | 30 | 0.156 | 562 | 605 | 97.851 | 4.793-5.32 | 0.183 | 52 | 0.185 | 507 | 561 | 99.643 | 5.32-6.07 | 0.303 | 32 | 0.228 | 469 | 501 | 100 | 6.07-7.266 | 0.228 | 18 | 0.222 | 423 | 441 | 100 | 7.266-9.649 | 0.136 | 14 | 0.193 | 336 | 351 | 99.715 | 9.649-19.834 | 0.176 | 6 | 0.195 | 244 | 252 | 99.206 |
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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 | 0.6952 | -0.1957 | -0.3827 | 3.8042 | 0.3666 | 0.924 | 0.047 | 0.092 | 0.0024 | -0.5602 | -0.0286 | -0.1464 | -0.0869 | 0.0039 | -0.0184 | 0.1123 | 0.0252 | 0.048 | 0.0337 | 0.0251 | 0.0455 | 25.882 | 35.292 | 14.899 | 2 | 0.6503 | -0.2396 | 0.0306 | 4.6016 | 0.1759 | 1.623 | -0.0121 | 0.03 | -0.0617 | 0.4737 | -0.0407 | 0.0947 | 0.1021 | -0.0479 | 0.0528 | 0.0859 | -0.0306 | 0.0302 | 0.0249 | -0.0123 | 0.0369 | 20.813 | 35.94 | 32.954 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA-2 - 151 | 2 | X-RAY DIFFRACTION | 2 | ALLB3 - 147 | | | | |
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