ソフトウェア | 名称 | バージョン | 分類 |
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Aimless | 0.5.8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: 1.9→48.66 Å / SU ML: 0.2 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 19.71 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1979 | 1251 | 4.87 % | Random selection |
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Rwork | 0.1636 | 24425 | - | - |
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obs | 0.1653 | 25676 | 99.98 % | - |
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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: 140.18 Å2 / Biso mean: 40.8004 Å2 / Biso min: 16.56 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.9→48.66 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2389 | 0 | 23 | 195 | 2607 |
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Biso mean | - | - | 41.81 | 40.79 | - |
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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_d0.018 | 2524 | X-RAY DIFFRACTION | f_angle_d0.883 | 3428 | X-RAY DIFFRACTION | f_chiral_restr0.049 | 371 | X-RAY DIFFRACTION | f_plane_restr0.005 | 450 | X-RAY DIFFRACTION | f_dihedral_angle_d12.416 | 1518 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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1.9-1.9761 | 0.3014 | 121 | 0.242 | 2667 | 2788 | 1.9761-2.066 | 0.244 | 134 | 0.2145 | 2650 | 2784 | 2.066-2.175 | 0.2312 | 152 | 0.1898 | 2668 | 2820 | 2.175-2.3112 | 0.2106 | 133 | 0.1749 | 2676 | 2809 | 2.3112-2.4897 | 0.1881 | 140 | 0.1589 | 2675 | 2815 | 2.4897-2.7402 | 0.1985 | 128 | 0.1644 | 2721 | 2849 | 2.7402-3.1367 | 0.2212 | 146 | 0.1673 | 2721 | 2867 | 3.1367-3.9516 | 0.1824 | 157 | 0.1486 | 2738 | 2895 | 3.9516-48.6756 | 0.1747 | 140 | 0.1508 | 2909 | 3049 |
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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 | 1.9109 | -0.8952 | -0.1617 | 2.8808 | -0.4188 | 1.9277 | -0.0737 | -0.089 | -0.1502 | 0.2833 | 0.1173 | 0.4002 | -0.0599 | -0.318 | -0.0411 | 0.2518 | 0.035 | 0.0408 | 0.2598 | 0.0198 | 0.2635 | -31.9939 | -9.0848 | -14.9269 | 2 | 1.8305 | -0.4213 | -0.3891 | 1.753 | 0.2227 | 0.3346 | 0.0076 | -0.7807 | -0.1897 | 0.8006 | 0.0605 | 0.1777 | 0.1124 | -0.2452 | 0.049 | 0.4861 | 0.0245 | 0.0929 | 0.4807 | 0.1101 | 0.2302 | -29.921 | -11.2095 | -2.731 | 3 | 1.802 | -0.6367 | 1.9587 | 1.2647 | -2.2965 | 4.6104 | -0.2707 | -0.6266 | 0.5023 | 0.7456 | -0.1576 | -0.0018 | -0.4238 | -0.0741 | -0.2388 | 0.6945 | 0.1234 | -0.0225 | 0.5054 | -0.1654 | 0.3542 | -27.6117 | 3.9173 | -0.3007 | 4 | 2.2209 | 0.6064 | 0.1636 | 0.9292 | 0.1258 | 1.3848 | -0.0276 | -0.6648 | 0.1186 | 0.4789 | 0.106 | 0.2867 | -0.1934 | -0.4485 | 0.0359 | 0.578 | 0.1119 | 0.0763 | 0.4525 | 0.0494 | 0.2893 | -31.3476 | -6.8232 | -4.2023 | 5 | 2.3436 | -0.3349 | -0.4849 | 0.9136 | 0.0446 | 1.6766 | -0.1277 | -0.0328 | -0.2567 | 0.2902 | 0.0723 | -0.0011 | 0.1494 | 0.0376 | 0.0511 | 0.2741 | 0.0251 | -0.0502 | 0.1788 | -0.0098 | 0.252 | -17.5956 | -13.7242 | -15.6662 | 6 | 1.3088 | 0.9929 | -0.2429 | 2.1798 | 0.3091 | 1.0549 | -0.0613 | -0.0388 | -0.1449 | 0.1993 | 0.0772 | -0.3114 | -0.0624 | 0.1847 | -0.0108 | 0.2652 | 0.0409 | -0.0845 | 0.2289 | -0.0171 | 0.2528 | -6.8016 | -5.1571 | -17.7805 | 7 | 3.3817 | 0.802 | -0.1061 | 0.8787 | 0.2486 | 0.7967 | 0.1429 | -0.1091 | 0.882 | 0.1787 | -0.0757 | 0.2613 | -0.3639 | -0.1103 | -0.1081 | 0.5508 | 0.0575 | -0.1004 | 0.2708 | -0.0231 | 0.5345 | -12.6343 | 11.5386 | -14.4582 |
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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 77 )) or ( chain 'A' and resid 999 ) or ( chain 'S' and resid 4 ) or ( chain 'S' and resid 10 ) or ( chain 'S' and resid 12 ) or ( chain 'S' and resid 13 ) or ( chain 'S' and resid 14 ) or ( chain 'S' and resid 19 ) or ( chain 'S' and resid 23 ) or ( chain 'S' and resid 25 ) or ( chain 'S' and resid 32 ) or ( chain 'S' and resid 40 ) or ( chain 'S' and resid 48 ) or ( chain 'S' and resid 57 ) or ( chain 'S' and resid 59 ) or ( chain 'S' and resid 60 ) or ( chain 'S' and resid 61 ) or ( chain 'S' and resid 65 ) or ( chain 'S' and resid 69 ) or ( chain 'S' and resid 75 ) or ( |
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