ソフトウェア | 名称 | バージョン | 分類 |
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Aimless | 0.5.12データスケーリング | PHENIX | | 精密化 | PDB_EXTRACT | 3.15 | データ抽出 | XDS | | データ削減 | Coot | | モデル構築 | |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: 2Q0I 解像度: 2.1→42.763 Å / SU ML: 0.26 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 22.98 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2359 | 920 | 4.83 % |
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Rwork | 0.1933 | 18111 | - |
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obs | 0.1954 | 19031 | 100 % |
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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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原子変位パラメータ | Biso max: 121.46 Å2 / Biso mean: 40.74 Å2 / Biso min: 16.45 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.1→42.763 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2372 | 0 | 24 | 159 | 2555 |
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Biso mean | - | - | 33.61 | 39.85 | - |
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残基数 | - | - | - | - | 301 |
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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_d0.011 | 2497 | X-RAY DIFFRACTION | f_angle_d0.455 | 3388 | X-RAY DIFFRACTION | f_chiral_restr0.038 | 367 | X-RAY DIFFRACTION | f_plane_restr0.002 | 445 | X-RAY DIFFRACTION | f_dihedral_angle_d8.15 | 1484 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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2.1001-2.2108 | 0.3245 | 119 | 0.2774 | 2521 | 2640 | 2.2108-2.3493 | 0.2818 | 127 | 0.2374 | 2568 | 2695 | 2.3493-2.5307 | 0.2144 | 125 | 0.205 | 2542 | 2667 | 2.5307-2.7853 | 0.2495 | 139 | 0.201 | 2557 | 2696 | 2.7853-3.1882 | 0.2486 | 151 | 0.1979 | 2551 | 2702 | 3.1882-4.0164 | 0.2002 | 125 | 0.1722 | 2611 | 2736 | 4.0164-42.7717 | 0.2288 | 134 | 0.1738 | 2761 | 2895 |
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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 | 3.298 | -0.0892 | 0.0489 | 2.6706 | 0.1019 | 1.9658 | -0.0706 | -0.2315 | -0.1737 | 0.27 | 0.0741 | 0.2671 | -0.0119 | -0.2555 | -0.0188 | 0.2564 | 0.0372 | 0.0576 | 0.244 | 0.032 | 0.2413 | -31.383 | -10.2889 | -11.3066 | 2 | 1.3545 | 0.7771 | 0.6936 | 3.142 | -3.522 | 6.052 | -0.0355 | -0.8853 | 0.4931 | 0.6547 | -0.109 | 0.4299 | -0.4985 | -0.0361 | 0.0602 | 0.5644 | 0.097 | 0.0004 | 0.438 | -0.1435 | 0.3081 | -27.3288 | 3.4069 | -0.1708 | 3 | 2.3126 | 0.7195 | -0.6076 | 1.5293 | 0.8798 | 1.8316 | -0.1722 | -0.3416 | 0.2911 | 0.4554 | 0.0358 | 0.1954 | 0.0937 | -0.3795 | 0.1268 | 0.4369 | 0.0883 | 0.0272 | 0.3488 | 0.0411 | 0.3263 | -31.0887 | -8.0816 | -3.5019 | 4 | 5.5683 | -0.7893 | -0.096 | 1.5267 | -0.1743 | 2.1751 | -0.16 | 0.089 | -1.1359 | 0.0769 | -0.0477 | 0.1504 | 0.6852 | -0.0307 | -0.1777 | 0.405 | 0.0369 | 0.0188 | 0.16 | 0.0717 | 0.3754 | -21.0984 | -24.1791 | -13.8113 | 5 | 1.9158 | 0.0821 | -0.4183 | 1.6078 | 0.3349 | 1.4319 | -0.0714 | -0.131 | -0.0701 | 0.3187 | 0.07 | -0.1397 | 0.0288 | 0.1766 | 0.0065 | 0.2363 | 0.03 | -0.0673 | 0.208 | -0.0088 | 0.2184 | -12.1465 | -8.6267 | -14.7971 | 6 | 1.7378 | 1.4439 | -0.2184 | 1.682 | 0.3784 | 0.6129 | -0.077 | 0.1205 | 0.0455 | 0.0638 | 0.0867 | -0.0462 | -0.0622 | 0.2245 | -0.0087 | 0.2554 | 0.0067 | -0.0483 | 0.2558 | -0.0152 | 0.2228 | -6.8221 | -4.1051 | -20.4699 | 7 | 0.9454 | -0.4471 | 0.3906 | 0.3726 | -0.2523 | 1.5644 | 0.131 | -0.223 | 0.7538 | -0.072 | -0.1591 | 0.0943 | -0.5887 | -0.2492 | 0.0253 | 0.7213 | 0.0275 | -0.0848 | 0.3794 | 0.0006 | 0.6911 | -12.2152 | 11.2151 | -14.0877 | 8 | 0.9412 | 0.0938 | 0.2181 | 2.3989 | -0.0009 | 2.5909 | 0.0075 | -0.2563 | 0.3315 | -0.0767 | 0.0167 | 0.2145 | -0.0816 | -0.0035 | 0.0257 | 0.5348 | -0.0784 | -0.1041 | 0.3776 | -0.1023 | 0.3793 | -7.4618 | 6.6935 | -6.5454 |
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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 18 through 102 )) or ( chain 'S' and resid 3 ) or ( chain 'S' and resid 6 ) or ( chain 'S' and resid 10 ) or ( chain 'S' and resid 12 ) or ( chain 'S' and resid 16 ) or ( chain 'S' and resid 28 ) or ( chain 'S' and resid 29 ) or ( chain 'S' and resid 32 ) or ( chain 'S' and resid 35 ) or ( chain 'S' and resid 38 ) or ( chain 'S' and resid 42 ) or ( chain 'S' and resid 54 ) or ( chain 'S' and resid 59 ) or ( chain 'S' and resid 60 ) or ( chain 'S' and resid 62 ) or ( chain 'S' and resid 63 ) or ( chain 'S' and resid 65 ) or ( chain 'S' and resid 72 ) or ( chain 'S' and resid 74 ) or ( |
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