ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.13_2998: ???)精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | PHENIX | | 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: 1.85→33.06 Å / SU ML: 0.29 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 29.3 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2474 | 1785 | 4.94 % |
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Rwork | 0.2109 | - | - |
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obs | 0.2128 | 36161 | 98.92 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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精密化ステップ | サイクル: LAST / 解像度: 1.85→33.06 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1273 | 0 | 14 | 46 | 1333 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.016 | 1300 | X-RAY DIFFRACTION | f_angle_d1.344 | 1750 | X-RAY DIFFRACTION | f_dihedral_angle_d4.091 | 1097 | X-RAY DIFFRACTION | f_chiral_restr0.087 | 201 | X-RAY DIFFRACTION | f_plane_restr0.007 | 217 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.85-1.8984 | 0.438 | 125 | 0.4073 | 2368 | X-RAY DIFFRACTION | 89 | 1.8984-1.9543 | 0.3704 | 137 | 0.3347 | 2672 | X-RAY DIFFRACTION | 99 | 1.9543-2.0174 | 0.3036 | 136 | 0.2673 | 2657 | X-RAY DIFFRACTION | 100 | 2.0174-2.0895 | 0.32 | 137 | 0.235 | 2683 | X-RAY DIFFRACTION | 100 | 2.0895-2.1731 | 0.2766 | 136 | 0.2239 | 2633 | X-RAY DIFFRACTION | 99 | 2.1731-2.272 | 0.2526 | 139 | 0.2194 | 2675 | X-RAY DIFFRACTION | 100 | 2.272-2.3917 | 0.245 | 142 | 0.2232 | 2692 | X-RAY DIFFRACTION | 100 | 2.3917-2.5415 | 0.2694 | 132 | 0.2344 | 2636 | X-RAY DIFFRACTION | 100 | 2.5415-2.7377 | 0.2307 | 143 | 0.2362 | 2667 | X-RAY DIFFRACTION | 100 | 2.7377-3.013 | 0.2411 | 141 | 0.2356 | 2690 | X-RAY DIFFRACTION | 100 | 3.013-3.4486 | 0.2453 | 136 | 0.2158 | 2664 | X-RAY DIFFRACTION | 100 | 3.4486-4.3433 | 0.2537 | 143 | 0.1824 | 2670 | X-RAY DIFFRACTION | 100 | 4.3433-33.06 | 0.2167 | 138 | 0.1896 | 2669 | X-RAY DIFFRACTION | 100 |
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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 | 2.8634 | -0.4102 | 0.3119 | 5.415 | 4.1878 | 3.5599 | 0.2328 | -0.2086 | -0.054 | 0.6204 | -0.5342 | 0.0023 | 0.5017 | -0.0232 | 0.4103 | 0.512 | -0.0706 | 0.0802 | 0.4427 | -0.04 | 0.3854 | 26.12 | 12.727 | 37.593 | 2 | 1.8689 | 0.985 | 0.9016 | 5.5311 | 5.4131 | 7.803 | 0.0382 | -0.1832 | -0.1472 | 1.5507 | -0.0482 | -0.3919 | 1.3711 | 0.0058 | 0.015 | 0.7721 | -0.0623 | 0.0124 | 0.4898 | 0.0096 | 0.3864 | 29.267 | 10.884 | 41.766 | 3 | 7.8562 | -6.2264 | 3.5481 | 5.7195 | -1.775 | 3.008 | 1.0449 | -1.3138 | -0.7557 | 2.0652 | -0.5089 | 1.6229 | 1.3634 | -0.4126 | 1.0415 | 1.6568 | -0.2886 | 0.4563 | 0.8835 | -0.0872 | 0.6534 | 17.726 | -1.389 | 45.966 | 4 | 1.4122 | 0.6095 | 0.5602 | 5.7449 | 2.3302 | 4.8232 | 0.1187 | -0.3403 | 0.1036 | 1.1014 | -0.4752 | 0.561 | 0.7957 | -0.6883 | 0.2467 | 0.4664 | -0.0942 | 0.1302 | 0.3929 | -0.1297 | 0.4399 | 21.506 | 8.313 | 32.947 | 5 | 4.8319 | 1.8837 | -1.499 | 9.2745 | -1.2267 | 8.2373 | 0.362 | 0.2599 | 0.6443 | -0.1536 | -0.1678 | 0.328 | -0.5261 | 0.3407 | 0.1364 | 0.3365 | 0.0345 | 0.0322 | 0.4219 | -0.0129 | 0.3694 | 29.798 | 12.999 | 17.434 | 6 | 7.7645 | 1.0736 | 2.0004 | 4.7008 | 3.9977 | 9.2216 | 0.1857 | 0.0635 | -0.7669 | -0.4495 | -0.5739 | 0.5559 | 0.4826 | -1.0307 | 0.441 | 0.5216 | 0.0377 | -0.0283 | 0.5957 | -0.1327 | 0.6173 | 18.917 | 8.639 | 18.948 | 7 | 2.818 | 2.6136 | 2.3905 | 8.6176 | 4.9737 | 3.3875 | -0.1628 | 0.1484 | 0.5094 | -1.2271 | -0.2679 | -0.0619 | -0.888 | -0.0927 | 0.4484 | 0.4839 | 0.0061 | 0.0018 | 0.4246 | -0.0773 | 0.5671 | 25.178 | 20.394 | 20.933 | 8 | 1.6174 | 1.4691 | -0.0246 | 6.1624 | 0.5537 | 9.0034 | 0.1181 | -0.2418 | -0.2215 | 0.6998 | -0.3449 | 0.3648 | 1.6507 | 0.0728 | 0.343 | 0.6169 | -0.005 | 0.0733 | 0.373 | -0.0509 | 0.5032 | 23.527 | -0.912 | 28.03 | 9 | 4.2353 | -0.9298 | -2.2669 | 3.1505 | 0.7989 | 7.0513 | 0.0876 | 0.1503 | 0.1849 | 0.4226 | -0.4258 | 0.9575 | 0.0219 | -1.4552 | 0.2756 | 0.3384 | -0.0249 | 0.1058 | 0.516 | -0.185 | 0.5951 | 17.584 | 12.719 | 29.212 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND RESID 10:27 )A10 - 27 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 28:46 )A28 - 46 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 47:55 )A47 - 55 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 56:88 )A56 - 88 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN A AND RESID 98:112 )A98 - 112 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN A AND RESID 131:151 )A131 - 151 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN A AND RESID 152:161 )A152 - 161 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN A AND RESID 162:180 )A162 - 180 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN A AND RESID 181:185 )A181 - 185 | | | | | | | | | | | | | | | | | | |
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