ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.20.1_4487: ???)精密化 | XDS | | データ削減 | Aimless | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.9→46.48 Å / 交差検証法: FREE R-VALUE / σ(F): 281.02 / 位相誤差: 24.11 / 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 | 0.2234 | 1031 | 4.8 % |
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Rwork | 0.1766 | - | - |
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obs | 0.1797 | 21470 | 100 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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Refine analyze | Luzzati coordinate error obs: 0.505 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.9→46.48 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6944 | 0 | 106 | 0 | 7050 |
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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 | 7184 | X-RAY DIFFRACTION | f_angle_d0.752 | 9780 | X-RAY DIFFRACTION | f_dihedral_angle_d8.699 | 998 | X-RAY DIFFRACTION | f_chiral_restr0.047 | 1116 | X-RAY DIFFRACTION | f_plane_restr0.007 | 1268 | | | | | |
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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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2.9-3.05 | 0.298 | 148 | 0.278 | 2917 | X-RAY DIFFRACTION | 95 | 3.05-3.24 | 0.3057 | 122 | 0.2655 | 2957 | X-RAY DIFFRACTION | 96 | 3.24-3.49 | 0.2777 | 186 | 0.2268 | 2877 | X-RAY DIFFRACTION | 94 | 3.5-3.85 | 0.2517 | 160 | 0.1962 | 2919 | X-RAY DIFFRACTION | 95 | 3.85-4.4 | 0.193 | 173 | 0.1631 | 2880 | X-RAY DIFFRACTION | 94 | 4.4-5.54 | 0.1685 | 128 | 0.1368 | 2943 | X-RAY DIFFRACTION | 96 | 5.55-46.48 | 0.2128 | 114 | 0.149 | 2946 | X-RAY DIFFRACTION | 96 |
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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 | 0.8345 | -0.1348 | -0.5749 | 2.8494 | -1.1195 | 2.0419 | -0.3703 | -0.2319 | -0.1402 | 0.4076 | 0.3304 | -0.2597 | 0.4221 | 0.3352 | 0.109 | 1.0622 | 0.1061 | -0.1471 | 0.6801 | 0.0212 | 0.5337 | -10.9863 | 38.0361 | 12.9877 | 2 | 3.797 | 0.8762 | -0.7618 | 2.689 | 0.1534 | 3.6166 | -0.0851 | 0.1027 | 0.1956 | -0.0864 | -0.1133 | -0.2994 | 0.4434 | 0.5666 | -0.0154 | 0.7004 | 0.055 | -0.016 | 0.3162 | 0.0453 | 0.5553 | -8.4615 | 48.4203 | -9.4895 | 3 | 0.7582 | 0.8227 | -0.269 | 2.6025 | -2.2034 | 2.3349 | -0.2503 | -0.07 | -0.2309 | -0.6786 | 0.1166 | -0.3291 | 1.1805 | 0.0451 | 0.2039 | 1.3357 | 0.2573 | -0.0064 | 0.6275 | -0.0611 | 0.5765 | -12.4066 | 27.69 | 0.5462 | 4 | 1.6986 | -0.4658 | -0.54 | 0.902 | 0.0859 | 0.4485 | 0.1005 | 0.6831 | 0.0402 | -0.1059 | -0.1728 | 0.2644 | 0.9564 | -0.5072 | -0.0172 | 1.2829 | -0.2915 | -0.1617 | 0.5313 | -0.0617 | 0.4198 | -35.2929 | 39.4028 | -5.386 | 5 | 1.6823 | 1.0457 | 0.6993 | 1.6516 | 0.1855 | 1.2853 | 0.3285 | 0.0888 | 0.422 | -1.2046 | -0.3894 | -0.2911 | 0.0858 | -0.8653 | -0.2469 | 0.6273 | -0.1328 | -0.0354 | 1.1965 | 0.0418 | 0.9163 | -63.9778 | 58.1621 | -10.082 | 6 | 2.494 | -0.698 | -0.8773 | 2.6277 | -0.6967 | 2.542 | -0.1203 | 0.2361 | 0.7944 | -0.0735 | 0.0655 | -0.3811 | 0.3439 | -0.2726 | 0.2958 | 0.3512 | -0.0059 | 0.0592 | 0.3004 | 0.0201 | 0.6642 | -37.3865 | 67.5589 | -1.4098 | 7 | 2.5892 | 0.4408 | 1.0562 | 2.9425 | -0.1547 | 0.5343 | -0.1319 | 0.1186 | 0.2496 | -0.2677 | -0.1829 | 0.336 | 0.0727 | -1.0389 | -0.0817 | 0.5318 | -0.1515 | -0.0052 | 1.2114 | 0.1045 | 0.5573 | -66.0477 | 66.8221 | -1.4346 | 8 | 2.1457 | -0.2969 | -0.2946 | 1.3727 | -0.0906 | 1.3456 | 0.1758 | -0.1173 | -0.0546 | 0.1885 | -0.3759 | -0.0337 | -0.0094 | -0.1775 | -0.017 | 0.5026 | 0.0249 | -0.088 | 0.5116 | 0.0717 | 0.4426 | -43.7322 | 69.1925 | 14.1837 | 9 | 5.0638 | -2.7045 | -0.4186 | 4.5811 | 0.3588 | 1.3132 | 0.0581 | -0.1782 | 0.5816 | 0.5074 | -0.0314 | -0.9724 | 0.1509 | -0.2142 | 0.2541 | 0.6663 | -0.0012 | -0.0171 | 0.5903 | 0.0548 | 0.4299 | -44.0527 | 70.4606 | 22.4871 | 10 | 1.1861 | -0.1942 | -0.091 | 2.5964 | 1.1325 | 0.7587 | -0.0418 | 0.2454 | -0.1661 | 0.5401 | -0.2666 | 0.2205 | 0.4367 | -1.0523 | 0.0719 | 0.7281 | -0.5227 | 0.0301 | 0.9816 | -0.0516 | 0.4994 | -62.7578 | 56.8387 | 6.1943 | 11 | 2.8374 | -0.1356 | -0.6005 | 1.6152 | 0.3165 | 1.4391 | 0.2384 | -0.0266 | 0.2639 | 0.2882 | -0.2232 | 0.1594 | 0.7064 | -0.5348 | 0.0324 | 0.7639 | -0.1568 | -0.0563 | 0.5299 | 0.0357 | 0.3498 | -43.7634 | 44.881 | 12.5168 | 12 | 2.7796 | -0.1522 | 0.3879 | 1.46 | 1.0112 | 1.594 | -0.3921 | 0.0418 | -0.2831 | -0.0368 | 0.2255 | -0.6413 | 1.3412 | 0.245 | -0.0483 | 1.0089 | -0.1205 | -0.0249 | 0.4202 | 0.0706 | 0.4071 | -33.1003 | 36.39 | 10.8038 |
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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 1 through 136 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 137 through 245 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 246 through 325 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 326 through 458 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 1 through 43 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 44 through 100 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 101 through 160 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 161 through 208 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 209 through 245 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 246 through 325 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 326 through 426 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 427 through 458 ) | | | | | | | | | | | |
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