ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | HKL-3000 | | データ収集 | HKL-3000 | | 位相決定 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: dev_1745)精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | PHENIX | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.299→34.735 Å / SU ML: 0.21 / Isotropic thermal model: mixed / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 23.89 / 立体化学のターゲット値: MLHL
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.243 | 1939 | 8.01 % | random |
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Rwork | 0.196 | - | - | - |
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all | 0.2 | 24220 | - | - |
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obs | 0.2 | 24220 | 97.1 % | - |
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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 mean: 54.7 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.299→34.735 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4278 | 0 | 29 | 135 | 4442 |
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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_d0.002 | 4440 | X-RAY DIFFRACTION | f_angle_d0.613 | 6004 | X-RAY DIFFRACTION | f_dihedral_angle_d14.3 | 1667 | X-RAY DIFFRACTION | f_chiral_restr0.023 | 663 | X-RAY DIFFRACTION | f_plane_restr0.002 | 777 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection obs | % reflection obs (%) |
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2.2986-2.3561 | 0.3143 | 119 | 0.2647 | 1438 | 1557 | 90 | 2.3561-2.4197 | 0.3169 | 135 | 0.259 | 1524 | 1659 | 94 | 2.4197-2.4909 | 0.3292 | 128 | 0.2525 | 1531 | 1659 | 95 | 2.4909-2.5713 | 0.2911 | 130 | 0.2516 | 1515 | 1645 | 94 | 2.5713-2.6632 | 0.2572 | 138 | 0.2295 | 1560 | 1698 | 97 | 2.6632-2.7698 | 0.2742 | 137 | 0.2194 | 1587 | 1724 | 97 | 2.7698-2.8957 | 0.2497 | 142 | 0.2261 | 1597 | 1739 | 98 | 2.8957-3.0483 | 0.2762 | 135 | 0.2253 | 1595 | 1730 | 99 | 3.0483-3.2392 | 0.2722 | 140 | 0.21 | 1611 | 1751 | 99 | 3.2392-3.4891 | 0.2282 | 144 | 0.2049 | 1628 | 1772 | 99 | 3.4891-3.8398 | 0.2512 | 146 | 0.1799 | 1631 | 1777 | 100 | 3.8398-4.3945 | 0.2059 | 150 | 0.1573 | 1658 | 1808 | 100 | 4.3945-5.533 | 0.2116 | 140 | 0.1655 | 1683 | 1823 | 100 | 5.533-34.7386 | 0.2267 | 155 | 0.1847 | 1723 | 1878 | 98 |
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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 | 1.6692 | 0.2611 | 0.5495 | 0.5319 | 0.0543 | 0.7681 | 0.048 | 0.3999 | 0.526 | -0.8422 | -0.0757 | 0.0704 | -0.1129 | -0.6477 | 0.0651 | 0.5907 | 0.0444 | -0.1753 | 0.4992 | -0.0195 | 0.5933 | 5.1044 | 63.8271 | 53.825 | 2 | 2.5833 | -0.7731 | 0.8259 | 3.2768 | 0.1262 | 1.4906 | 0.03 | 0.3374 | 0.3783 | -0.2929 | -0.1036 | -0.2184 | -0.028 | 0.283 | 0.028 | 0.3291 | -0.0137 | -0.0002 | 0.2878 | 0.0534 | 0.24 | 24.8045 | 60.0249 | 59.1166 | 3 | 3.5831 | 0.0874 | -0.2183 | 1.8971 | -0.3445 | 5.7078 | 0.1783 | 0.1451 | -0.6036 | -0.2927 | 0.1177 | -0.7646 | 0.7661 | -0.0336 | -0.213 | 0.4769 | 0.0841 | 0.0464 | 0.3636 | -0.0687 | 0.5585 | 46.2196 | 42.2778 | 63.5099 | 4 | 0.8198 | -0.0205 | 0.6559 | 1.9397 | -0.0042 | 1.4896 | -0.1525 | -0.0618 | 0.0166 | 0.23 | 0.1667 | 0.0119 | 0.2001 | -0.1571 | -0.0327 | 0.3113 | 0.0222 | 0.0314 | 0.3586 | -0.0177 | 0.1983 | 21.9032 | 50.7204 | 69.5962 | 5 | 0.6932 | 0.3799 | 0.1306 | 2.1471 | 0.4492 | 0.8159 | -0.1398 | -0.841 | 0.2566 | 0.0186 | -0.0893 | 0.7995 | -0.4434 | -0.0832 | 0.1697 | 0.4249 | 0.0659 | 0.0394 | 0.5952 | -0.1283 | 0.6048 | -3.0043 | 52.3159 | 64.0165 | 6 | 1.6116 | 0.2025 | -0.6632 | 1.75 | 0.7092 | 1.8243 | 0.0412 | -0.0459 | 0.0103 | 0.3877 | -0.1812 | 0.5362 | 0.1047 | -0.0795 | 0.1431 | 0.306 | -0.0199 | 0.0455 | 0.3202 | -0.0297 | 0.3456 | 5.1674 | 35.3634 | 57.0352 | 7 | 3.4333 | -0.5897 | 1.1974 | 3.812 | -1.1674 | 3.7883 | 0.3188 | -0.0717 | -0.7858 | 0.4269 | -0.1236 | -0.9822 | 0.5679 | 0.6562 | -0.0509 | 0.3701 | 0.0263 | -0.1498 | 0.3546 | 0.061 | 0.5429 | 27.5135 | 18.6238 | 48.9576 | 8 | 0.6243 | 1.1207 | 0.7294 | 2.2449 | 1.5926 | 1.0457 | -0.1711 | -0.1464 | -0.0447 | -0.2131 | 0.2794 | -0.3716 | -0.2888 | 0.4461 | -0.0777 | 0.4254 | -0.0386 | 0.0411 | 0.4761 | 0.021 | 0.2425 | 23.9881 | 42.3169 | 43.8774 | 9 | 0.9377 | -1.0061 | -0.8956 | 1.3714 | 0.6623 | 0.9672 | 0.0392 | 0.2762 | 0.0074 | -0.3421 | -0.2403 | 0.739 | -0.3339 | -0.2395 | 0.1514 | 0.2765 | 0.025 | -0.0263 | 0.4127 | -0.0703 | 0.4258 | 2.3111 | 39.3223 | 48.2837 |
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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 0 through 30 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 31 through 117 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 118 through 176 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 177 through 254 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 0 through 30 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 31 through 115 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 116 through 176 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 177 through 216 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 217 through 254 ) | | | | | | | | |
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