ソフトウェア | 名称 | バージョン | 分類 |
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DENZO | | データ収集 | SCALEPACK | | データスケーリング | MOLREP | | 位相決定 | PHENIX | 1.12_2829精密化 | PDB_EXTRACT | 3.22 | データ抽出 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.399→41.593 Å / SU ML: 0.25 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 19.34
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2007 | 3125 | 5.03 % | random selection |
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Rwork | 0.1683 | - | - | - |
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obs | 0.1699 | 62119 | 99.35 % | - |
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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 |
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原子変位パラメータ | Biso max: 163.05 Å2 / Biso mean: 45.4487 Å2 / Biso min: 18.62 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.399→41.593 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5739 | 0 | 108 | 361 | 6208 |
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Biso mean | - | - | 46.39 | 48.6 | - |
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残基数 | - | - | - | - | 691 |
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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_d0.007 | 6039 | X-RAY DIFFRACTION | f_angle_d0.917 | 8176 | X-RAY DIFFRACTION | f_chiral_restr0.051 | 858 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1042 | X-RAY DIFFRACTION | f_dihedral_angle_d17.817 | 3550 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.3986-2.4361 | 0.2923 | 132 | 0.2568 | 2612 | 2744 | 99 | 2.4361-2.476 | 0.2953 | 130 | 0.2488 | 2667 | 2797 | 100 | 2.476-2.5187 | 0.2508 | 128 | 0.2356 | 2621 | 2749 | 100 | 2.5187-2.5645 | 0.2719 | 118 | 0.2351 | 2683 | 2801 | 100 | 2.5645-2.6138 | 0.2627 | 153 | 0.2283 | 2599 | 2752 | 99 | 2.6138-2.6672 | 0.2582 | 166 | 0.2177 | 2613 | 2779 | 99 | 2.6672-2.7251 | 0.2439 | 145 | 0.2146 | 2622 | 2767 | 99 | 2.7251-2.7885 | 0.2404 | 137 | 0.2042 | 2629 | 2766 | 99 | 2.7885-2.8582 | 0.2676 | 134 | 0.2009 | 2628 | 2762 | 99 | 2.8582-2.9355 | 0.2281 | 151 | 0.1896 | 2625 | 2776 | 99 | 2.9355-3.0219 | 0.2288 | 132 | 0.1871 | 2634 | 2766 | 99 | 3.0219-3.1194 | 0.2195 | 142 | 0.1848 | 2645 | 2787 | 98 | 3.1194-3.2308 | 0.2205 | 146 | 0.183 | 2626 | 2772 | 99 | 3.2308-3.3601 | 0.2225 | 142 | 0.1687 | 2698 | 2840 | 100 | 3.3601-3.513 | 0.2051 | 145 | 0.1492 | 2663 | 2808 | 100 | 3.513-3.6981 | 0.1754 | 159 | 0.1429 | 2684 | 2843 | 100 | 3.6981-3.9296 | 0.1745 | 154 | 0.1321 | 2690 | 2844 | 100 | 3.9296-4.2327 | 0.1535 | 134 | 0.1243 | 2742 | 2876 | 100 | 4.2327-4.6582 | 0.1574 | 148 | 0.1187 | 2743 | 2891 | 100 | 4.6582-5.331 | 0.1455 | 129 | 0.128 | 2784 | 2913 | 100 | 5.331-6.712 | 0.1889 | 137 | 0.1773 | 2819 | 2956 | 100 | 6.712-41.5994 | 0.1781 | 163 | 0.1858 | 2967 | 3130 | 99 |
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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 | 2.1758 | 0.8087 | -0.1702 | 2.4651 | -0.4013 | 1.8053 | -0.0656 | 0.4729 | 0.4846 | -0.1358 | 0.0719 | 0.1281 | -0.3394 | -0.1448 | -0.0507 | 0.3353 | 0.0762 | 0.0321 | 0.3361 | 0.1078 | 0.4318 | -63.0709 | 52.8875 | -1.4051 | 2 | 2.3143 | 0.5788 | -0.6293 | 0.9615 | -0.2042 | 1.3876 | 0.0252 | 0.0782 | 0.5332 | 0.1043 | 0.0139 | 0.1233 | -0.2816 | 0.0773 | -0.0107 | 0.3946 | -0.0942 | 0 | 0.2731 | 0.0392 | 0.3559 | -37.6631 | 59.4577 | -2.4294 | 3 | 2.541 | 0.6191 | -0.9306 | 1.1563 | -0.2321 | 1.1637 | -0.0366 | -0.0015 | 0.1469 | -0.0101 | 0.0336 | 0.0188 | -0.2241 | 0.2446 | 0.0306 | 0.3038 | -0.084 | -0.0277 | 0.3021 | 0.0465 | 0.256 | -35.3888 | 51.2074 | -5.1889 | 4 | 1.2771 | 1.3387 | -0.1828 | 2.3848 | -0.1948 | 1.7672 | -0.0225 | 0.0424 | 0.1067 | 0.0097 | 0.0694 | 0.2157 | 0.1033 | -0.1186 | -0.0505 | 0.3066 | -0.0399 | 0.0419 | 0.2541 | 0.0633 | 0.2535 | -45.4629 | 23.4118 | -19.3211 | 5 | 2.155 | -0.2954 | 0.1348 | 1.8069 | 0.0699 | 1.6503 | -0.2173 | 0.0382 | -0.0786 | -0.2606 | 0.0721 | 0.4164 | 0.4104 | -0.6742 | 0.1276 | 0.4201 | -0.1268 | 0.0057 | 0.3861 | 0.0616 | 0.3659 | -54.1169 | 17.0186 | -10.6646 | 6 | 0.709 | 0.1079 | -0.5031 | 0.7243 | -0.0528 | 1.9036 | -0.0924 | -0.0659 | -0.0771 | 0.0307 | 0.0046 | -0.0127 | 0.27 | 0.022 | 0.0837 | 0.2682 | 0.0208 | 0.0232 | 0.192 | 0.0648 | 0.2492 | -51.494 | 16.2197 | 6.4248 | 7 | 2.0658 | 0.2452 | -0.6733 | 0.945 | 0.1171 | 1.3642 | 0.0422 | -0.0274 | 0.0778 | 0.0955 | -0.0495 | 0.0946 | -0.1814 | -0.0692 | 0.0126 | 0.2949 | 0.0316 | 0.0403 | 0.2172 | 0.0268 | 0.2349 | -55.4147 | 31.2747 | 11.2441 |
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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 57 through 128 )A57 - 128 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 129 through 243 )A129 - 243 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 244 through 409 )A244 - 409 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 56 through 131 )B56 - 131 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 132 through 170 )B132 - 170 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 171 through 342 )B171 - 342 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 343 through 409 )B343 - 409 | | | | | | | | | | | | | | |
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