ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.8.3_1479精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHASER | | 位相決定 | CBASS | | データ収集 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 4ITY 解像度: 1.65→45.783 Å / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 27.97 / 立体化学のターゲット値: TWIN_LSQ_F
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2125 | 2019 | 5.01 % |
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Rwork | 0.1873 | - | - |
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obs | 0.189 | 40270 | 99.51 % |
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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: 1.65→45.783 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2312 | 0 | 36 | 146 | 2494 |
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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_d0.003 | 2404 | X-RAY DIFFRACTION | f_angle_d0.806 | 3262 | X-RAY DIFFRACTION | f_dihedral_angle_d14.693 | 906 | X-RAY DIFFRACTION | f_chiral_restr0.028 | 373 | X-RAY DIFFRACTION | f_plane_restr0.003 | 419 | | | | | |
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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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1.651-1.6923 | 0.3081 | 137 | 0.309 | 2620 | X-RAY DIFFRACTION | 90 | 1.6923-1.738 | 0.2917 | 127 | 0.2904 | 2762 | X-RAY DIFFRACTION | 95 | 1.738-1.7891 | 0.3431 | 140 | 0.2695 | 2749 | X-RAY DIFFRACTION | 95 | 1.7891-1.8469 | 0.2876 | 135 | 0.2536 | 2712 | X-RAY DIFFRACTION | 95 | 1.8469-1.9128 | 0.2468 | 136 | 0.2374 | 2747 | X-RAY DIFFRACTION | 95 | 1.9128-1.9894 | 0.2655 | 138 | 0.238 | 2771 | X-RAY DIFFRACTION | 95 | 1.9894-2.0798 | 0.2466 | 139 | 0.2315 | 2718 | X-RAY DIFFRACTION | 95 | 2.0798-2.1894 | 0.2477 | 165 | 0.2168 | 2728 | X-RAY DIFFRACTION | 94 | 2.1894-2.3264 | 0.2149 | 135 | 0.2084 | 2741 | X-RAY DIFFRACTION | 95 | 2.3264-2.5058 | 0.2385 | 136 | 0.2033 | 2724 | X-RAY DIFFRACTION | 95 | 2.5058-2.7576 | 0.2082 | 162 | 0.1945 | 2738 | X-RAY DIFFRACTION | 94 | 2.7576-3.1557 | 0.2271 | 151 | 0.1884 | 2736 | X-RAY DIFFRACTION | 95 | 3.1557-3.9721 | 0.186 | 155 | 0.1524 | 2723 | X-RAY DIFFRACTION | 95 | 3.9721-22.2355 | 0.1716 | 160 | 0.1449 | 2726 | X-RAY DIFFRACTION | 94 |
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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 | 0.088 | 0.049 | 0.0249 | 0.0953 | 0.1487 | 0.1047 | -0.0799 | 0.1547 | -0.5329 | -0.187 | 0.0992 | -0.028 | -0.0518 | 0.044 | -0 | 0.2657 | -0.0168 | -0.0198 | 0.1666 | -0.0766 | 0.1739 | -17.5007 | -23.305 | 29.4439 | 2 | -0.0121 | -0.0342 | 0.0171 | -0.0178 | 0.0111 | -0.0046 | -0.3412 | 0.1931 | 0.0865 | -0.2863 | -0.0842 | 0.0451 | 0.1147 | -0.151 | -0 | -0.1224 | -0.1009 | -0.836 | 0.3836 | -0.1047 | -0.4037 | -34.4559 | -10.2603 | 21.3672 | 3 | -0.0071 | 0.0029 | 0.0107 | 0.0008 | -0.0166 | -0.0183 | -0.2646 | -0.0385 | -0.2481 | -0.0959 | -0.0566 | 0.2001 | 0.1283 | -0.0495 | -0 | 0.1503 | -0.0491 | -0.041 | 0.1521 | -0.0252 | 0.2939 | -32.4336 | -21.4217 | 34.3578 | 4 | 0.2555 | -0.0763 | 0.1475 | 0.4306 | 0.0316 | 0.0545 | -0.0539 | -0.0864 | 0.0484 | -0.0859 | -0.0009 | 0.1747 | 0.0042 | -0.0062 | 0 | 0.1133 | -0.0055 | -0.0218 | 0.129 | -0.0177 | 0.1199 | -24.3801 | -8.2175 | 42.5403 | 5 | -0.0059 | -0.0005 | 0.0051 | -0.0074 | -0.0059 | 0.0001 | -0.0262 | 0.1898 | 0.1026 | -0.0832 | -0.0307 | 0.0017 | -0.1033 | -0.1327 | -0 | 0.2175 | -0.0304 | 0.0479 | 0.237 | -0.0081 | 0.1399 | -10.5667 | -2.8265 | 30.4288 | 6 | -0.0046 | 0.062 | 0.0051 | 0.0721 | 0.0431 | 0.0092 | -0.0991 | 0.0008 | -0.1838 | -0.1371 | 0.0481 | -0.2924 | 0.0256 | -0.0539 | 0 | 0.1635 | -0.0192 | -0.0015 | 0.1411 | -0.0157 | 0.1201 | -11.0405 | -13.8587 | 38.4547 | 7 | -0.0096 | -0.0081 | 0.0308 | -0.0063 | 0.0139 | -0.0052 | -0.0872 | -0.1373 | -0.1614 | -0.1014 | -0.0845 | -0.1758 | -0.0366 | -0.0571 | 0 | 0.1547 | -0.0165 | 0.0392 | 0.1317 | -0.0394 | 0.2458 | -5.1206 | -18.995 | 36.9815 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 13 through 61 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 62 through 82 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 83 through 102 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 103 through 246 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 247 through 264 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 265 through 301 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 302 through 322 ) | | | | | | |
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