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 | SHELX | | モデル構築 | ARP/wARP | | モデル構築 | Coot | | モデル構築 | REFMAC | 5.5.0054精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | SHELX | | 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: 1.66→25.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.746 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.1 / ESU R Free: 0.1 / 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 | 0.2015 | 545 | 4.8 % | RANDOM |
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Rwork | 0.16278 | - | - | - |
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all | 0.17 | 11446 | - | - |
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obs | 0.16471 | 10901 | 98.27 % | - |
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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: 8.882 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.45 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.14 Å2 | 0 Å2 |
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3- | - | - | 1.31 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.66→25.5 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 829 | 0 | 0 | 102 | 931 |
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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_d0.019 | 0.022 | 846 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 564 | X-RAY DIFFRACTION | r_angle_refined_deg1.596 | 1.956 | 1145 | X-RAY DIFFRACTION | r_angle_other_deg0.914 | 3 | 1385 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.077 | 5 | 104 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.495 | 24.872 | 39 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.05 | 15 | 147 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg21.505 | 15 | 3 | X-RAY DIFFRACTION | r_chiral_restr0.105 | 0.2 | 132 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.021 | 932 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 167 | 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_it1.143 | 1.5 | 521 | X-RAY DIFFRACTION | r_mcbond_other0.35 | 1.5 | 212 | X-RAY DIFFRACTION | r_mcangle_it1.954 | 2 | 851 | X-RAY DIFFRACTION | r_scbond_it2.623 | 3 | 325 | X-RAY DIFFRACTION | r_scangle_it4.104 | 4.5 | 294 | 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: 1.659→1.702 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.147 | 39 | - |
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Rwork | 0.188 | 748 | - |
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obs | - | - | 92.7 % |
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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 | 0.0558 | -0.4214 | -0.3841 | 10.0506 | 4.6372 | 3.3637 | 0.0242 | 0.0416 | 0.0007 | -0.2515 | -0.0848 | 0.0143 | -0.2002 | -0.046 | 0.0606 | 0.0998 | 0.0148 | -0.0014 | 0.1651 | 0.0085 | 0.1353 | 2.7494 | 4.9026 | 25.7684 | 2 | 3.9191 | -0.5591 | 4.379 | 0.5201 | -1.1172 | 5.9108 | -0.0345 | 0.0704 | -0.0603 | 0.1436 | -0.0495 | -0.0798 | -0.108 | 0.1192 | 0.084 | 0.1023 | -0.0102 | 0.0068 | 0.0862 | 0.0055 | 0.1072 | 3.1041 | -6.6954 | 39.9448 | 3 | 2.4607 | 0.572 | 3.4524 | 1.0647 | 1.3147 | 11.7342 | -0.0196 | -0.2253 | -0.0719 | 0.1434 | -0.0295 | -0.0245 | 0.0421 | -0.1028 | 0.0491 | 0.1076 | -0.0042 | 0.0029 | 0.0996 | 0.006 | 0.1149 | 3.7766 | -2.3082 | 44.1963 | 4 | 3.5957 | 1.1963 | -5.7609 | 2.4518 | 0.6261 | 22.4256 | -0.0048 | 0.1507 | -0.0062 | -0.1802 | 0.0266 | 0.0407 | 0.1196 | -0.273 | -0.0217 | 0.1017 | 0.0102 | -0.007 | 0.1222 | -0.0037 | 0.1454 | 6.4217 | -2.7188 | 26.1358 | 5 | 1.3902 | -0.7905 | -2.8675 | 1.4115 | 3.1048 | 12.6477 | -0.0423 | -0.0144 | -0.0989 | 0.1124 | -0.0014 | -0.0495 | 0.2457 | 0.1461 | 0.0437 | 0.081 | -0.0092 | -0.0055 | 0.0789 | 0.0116 | 0.1103 | 7.9081 | 0.6513 | 37.1172 | 6 | 2.6111 | -1.1791 | -0.509 | 8.7255 | 4.9478 | 8.5229 | -0.1472 | -0.5343 | -0.0896 | 0.5668 | -0.054 | -0.2185 | 0.2041 | -0.1156 | 0.2011 | 0.1709 | -0.0406 | -0.0615 | 0.1901 | 0.0393 | 0.1031 | 12.8228 | 1.3407 | 54.1146 | 7 | 0.9833 | -2.1873 | 1.0213 | 6.5355 | -1.1751 | 1.784 | 0.078 | 0.0197 | 0.1574 | -0.1355 | -0.2372 | -0.3954 | 0.0986 | -0.1057 | 0.1592 | 0.0949 | -0.0272 | 0.0052 | 0.1322 | 0.0469 | 0.2074 | 19.1937 | -5.1964 | 40.0245 | 8 | 5.9278 | 1.1999 | -0.9895 | 5.256 | 1.5461 | 2.8707 | 0.0978 | 0.0865 | -0.264 | -0.1056 | -0.1832 | -0.4527 | -0.0984 | 0.0436 | 0.0854 | 0.0779 | -0.0247 | 0.0008 | 0.1089 | 0.019 | 0.1233 | 14.7081 | 5.5576 | 36.412 | 9 | 3.5683 | -0.3645 | 2.7366 | 3.3992 | -1.5835 | 2.6057 | 0.0393 | -0.0592 | 0.0228 | 0.2446 | -0.1266 | -0.1784 | -0.0712 | -0.0041 | 0.0873 | 0.1196 | -0.0212 | -0.023 | 0.1175 | 0.0097 | 0.1021 | 11.7124 | 11.1723 | 45.1928 | 10 | 6.3223 | 0.7697 | -3.1539 | 10.0327 | 5.0924 | 6.9998 | -0.28 | -0.3676 | -0.504 | 0.8054 | 0.1302 | -1.0982 | 0.2858 | 0.8894 | 0.1498 | 0.1723 | -0.012 | -0.1048 | 0.2474 | 0.0945 | 0.3186 | 25.4097 | 4.1841 | 48.4555 | 11 | 5.3739 | -3.4158 | 2.3022 | 7.4287 | -2.0513 | 5.5023 | -0.0054 | -0.1873 | 0.025 | 0.3623 | -0.1052 | -0.4333 | -0.2041 | 0.3759 | 0.1106 | 0.0976 | -0.0475 | -0.0458 | 0.1473 | 0.0307 | 0.1142 | 18.0738 | 12.6799 | 46.1571 | 12 | 5.9641 | -4.0097 | -2.3356 | 6.437 | 1.4332 | 2.9312 | -0.0504 | -0.0897 | -0.1239 | 0.0858 | -0.1252 | -0.3731 | 0.0572 | 0.0965 | 0.1755 | 0.0552 | -0.0312 | -0.0076 | 0.0959 | 0.0434 | 0.1422 | 18.7355 | 7.4047 | 38.1959 | 13 | 9.7745 | -6.512 | -5.4044 | 7.7518 | 4.7506 | 4.994 | -0.0665 | -0.3623 | 0.0574 | 0.2893 | 0.1481 | -0.645 | 0.1145 | 0.26 | -0.0816 | 0.1035 | -0.0354 | -0.0393 | 0.1174 | 0.0576 | 0.1767 | 18.5951 | 0.8624 | 46.1981 | 14 | 5.967 | -0.0024 | 2.7736 | 4.2833 | 0.2659 | 10.6553 | -0.0093 | -0.4294 | 0.2533 | 0.2687 | -0.061 | 0.0567 | -0.3155 | -0.3407 | 0.0703 | 0.1073 | -0.0111 | 0.0025 | 0.1042 | 0.004 | 0.1035 | 5.5236 | 9.4125 | 46.9082 | 15 | 9.8302 | -0.5074 | -4.8387 | 6.204 | -0.5799 | 8.3145 | -0.1486 | -0.0317 | -0.4919 | -0.1589 | -0.0321 | -0.2917 | 0.3588 | 0.3373 | 0.1807 | 0.0674 | -0.0134 | -0.0088 | 0.0848 | 0.0018 | 0.102 | 11.9996 | 2.1135 | 35.026 |
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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 | A3 - 10 | 2 | X-RAY DIFFRACTION | 2 | A11 - 19 | 3 | X-RAY DIFFRACTION | 3 | A20 - 26 | 4 | X-RAY DIFFRACTION | 4 | A27 - 31 | 5 | X-RAY DIFFRACTION | 5 | A32 - 44 | 6 | X-RAY DIFFRACTION | 6 | A45 - 49 | 7 | X-RAY DIFFRACTION | 7 | A50 - 55 | 8 | X-RAY DIFFRACTION | 8 | A56 - 60 | 9 | X-RAY DIFFRACTION | 9 | A61 - 67 | 10 | X-RAY DIFFRACTION | 10 | A68 - 73 | 11 | X-RAY DIFFRACTION | 11 | A74 - 79 | 12 | X-RAY DIFFRACTION | 12 | A80 - 87 | 13 | X-RAY DIFFRACTION | 13 | A88 - 96 | 14 | X-RAY DIFFRACTION | 14 | A97 - 101 | 15 | X-RAY DIFFRACTION | 15 | A102 - 106 | | | | | | | | | | | | | | | |
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