ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.19.2-4158) | 精密化 | HKL-2000 | | データ削減 | HKL-2000 | | 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 開始モデル: AlphaFold 解像度: 2.2→22.38 Å / SU ML: 0.23 / 交差検証法: NONE / σ(F): 1.35 / 位相誤差: 23.03 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2157 | 1884 | 5.02 % |
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Rwork | 0.179 | - | - |
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obs | 0.1809 | 37525 | 99.95 % |
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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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精密化ステップ | サイクル: LAST / 解像度: 2.2→22.38 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4078 | 0 | 0 | 353 | 4431 |
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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_d0.004 | 4182 | X-RAY DIFFRACTION | f_angle_d0.678 | 5642 | X-RAY DIFFRACTION | f_dihedral_angle_d13.453 | 1512 | X-RAY DIFFRACTION | f_chiral_restr0.05 | 584 | X-RAY DIFFRACTION | f_plane_restr0.004 | 723 | | | | | |
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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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2.2-2.26 | 0.2711 | 141 | 0.2434 | 2714 | X-RAY DIFFRACTION | 99 | 2.26-2.33 | 0.2874 | 148 | 0.2291 | 2707 | X-RAY DIFFRACTION | 100 | 2.33-2.4 | 0.2393 | 143 | 0.2284 | 2725 | X-RAY DIFFRACTION | 100 | 2.4-2.49 | 0.293 | 142 | 0.2193 | 2708 | X-RAY DIFFRACTION | 100 | 2.49-2.59 | 0.2846 | 146 | 0.2198 | 2748 | X-RAY DIFFRACTION | 100 | 2.59-2.7 | 0.2324 | 143 | 0.2146 | 2730 | X-RAY DIFFRACTION | 100 | 2.7-2.85 | 0.2678 | 140 | 0.2108 | 2722 | X-RAY DIFFRACTION | 100 | 2.85-3.02 | 0.2508 | 145 | 0.2027 | 2724 | X-RAY DIFFRACTION | 100 | 3.02-3.26 | 0.2295 | 143 | 0.1906 | 2741 | X-RAY DIFFRACTION | 100 | 3.26-3.58 | 0.2035 | 147 | 0.1622 | 2742 | X-RAY DIFFRACTION | 100 | 3.58-4.1 | 0.1781 | 143 | 0.1416 | 2750 | X-RAY DIFFRACTION | 100 | 4.1-5.15 | 0.1634 | 151 | 0.1333 | 2779 | X-RAY DIFFRACTION | 100 | 5.16-22.38 | 0.1876 | 152 | 0.1716 | 2851 | X-RAY DIFFRACTION | 100 |
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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 | 0.1186 | 0.0005 | -0.0979 | 0.3616 | 0.0733 | 0.3335 | 0.1167 | -0.2665 | -0.07 | 0.1369 | -0.4881 | 0.1524 | 0.1992 | -0.6384 | -0.431 | 0.3287 | -0.2481 | -0.0764 | 0.3356 | 0.0232 | 0.4066 | 110.2148 | 64.3884 | 20.5188 | 2 | 0.3458 | 0.1213 | 0.3038 | 0.3358 | 0.0394 | 0.5485 | 0.4646 | -0.7371 | 0.1066 | 0.2968 | -0.5295 | 0.1496 | 0.4994 | -0.8474 | 0.4034 | 0.1671 | -0.1081 | -0.0626 | 0.2096 | -0.0153 | 0.3194 | 116.5406 | 68.5913 | 22.7763 | 3 | 0.0018 | 0.0206 | -0.022 | 0.1928 | -0.156 | 0.13 | -0.0342 | -0.0905 | 0.1427 | 0.0236 | -0.2185 | 0.0302 | 0.0827 | -0.052 | -0.0709 | 0.1778 | -0.0229 | -0.0042 | 0.3485 | -0.1252 | 0.2922 | 111.4451 | 76.5065 | 22.1209 | 4 | 0.6685 | 0.3126 | 0.3547 | 0.5266 | 0.1302 | 0.5745 | 0.2834 | -0.6144 | 0.2698 | -0.0111 | -0.5391 | 0.3235 | 0.2688 | -0.9494 | -0.3693 | 0.193 | -0.2644 | -0.0046 | 0.515 | -0.1853 | 0.272 | 115.5854 | 75.8085 | 30.0802 | 5 | 0.0451 | -0.0343 | 0.0355 | 0.0558 | 0.0453 | 0.1258 | -0.0661 | -0.2332 | 0.1349 | 0.1153 | -0.2843 | 0.1261 | 0.0005 | -0.4332 | -0.1966 | 0.2397 | -0.3046 | -0.067 | 0.5243 | -0.6219 | -0.0759 | 122.7948 | 85.7424 | 40.7048 | 6 | 0.0078 | -0.0082 | -0.0101 | 0.0133 | -0.0174 | 0.1352 | 0.0318 | -0.2562 | 0.1234 | 0.0298 | 0.0922 | 0.0406 | 0.0245 | -0.3879 | 0.1737 | 0.3996 | -0.3674 | 0.1304 | 0.7679 | -0.4976 | 0.0986 | 111.8936 | 79.9976 | 40.7445 | 7 | 0.1734 | -0.0441 | 0.0444 | 0.0706 | 0.0101 | 0.1812 | -0.0703 | 0.1248 | 0.0049 | -0.1803 | -0.0848 | -0.0694 | -0.2067 | -0.0032 | -0.2009 | 0.2768 | -0.0588 | -0.0776 | 0.1708 | 0.038 | 0.1799 | 132.2465 | 82.9092 | 6.4517 | 8 | 0.3829 | -0.0126 | 0.324 | 0.0383 | -0.0097 | 0.1364 | -0.1037 | -0.0113 | 0.0877 | -0.1697 | 0.0842 | 0.2264 | -0.0767 | 0.0324 | 0.0384 | 0.2244 | -0.0219 | -0.0802 | 0.159 | -0.01 | 0.2197 | 127.874 | 76.6023 | 13.7712 | 9 | 0.0405 | -0.0256 | 0.0342 | 0.0602 | -0.0237 | 0.0115 | 0.028 | 0.0383 | -0.1984 | 0.0125 | 0.1237 | 0.1016 | 0.0625 | 0.0115 | 0.1175 | 0.1614 | -0.032 | -0.0575 | 0.1335 | -0.0295 | 0.1514 | 130.0291 | 69.4357 | 9.8606 | 10 | 0.2362 | -0.0857 | 0.2731 | 0.0597 | -0.0369 | 0.159 | -0.0415 | 0.0253 | -0.0272 | 0.2128 | 0.1055 | -0.1653 | -0.0173 | 0.1851 | 0.065 | 0.2132 | -0.0326 | -0.0621 | 0.1789 | -0.0318 | 0.1735 | 140.3558 | 78.4317 | 15.3734 | 11 | 0.033 | 0.0716 | -0.0321 | 0.0537 | -0.037 | 0.0936 | 0.4078 | -0.0495 | -0.2809 | 0.28 | -0.0743 | 0.0615 | 0.0633 | -0.0966 | 0.1429 | 0.1554 | -0.0503 | -0.2117 | 0.1414 | 0.048 | 0.1325 | 126.1075 | 62.0294 | 17.3587 | 12 | 0.2513 | 0.0413 | -0.2767 | 0.0988 | -0.0577 | 0.3249 | 0.3146 | -0.0519 | -0.2348 | 0.1058 | 0.0128 | -0.0799 | 0.1115 | 0.152 | 0.2329 | 0.1899 | 0.0372 | -0.2001 | 0.136 | -0.0348 | 0.275 | 143.7886 | 66.3633 | 18.2177 | 13 | 0.1369 | -0.0187 | 0.0452 | 0.0105 | -0.0208 | 0.0813 | 0.4483 | -0.1538 | -0.3589 | 0.0187 | 0.134 | -0.063 | 0.4382 | -0.0145 | 0.4986 | 0.3765 | -0.0798 | -0.3864 | 0.1915 | 0.3176 | 0.1701 | 143.7408 | 61.6797 | 27.6108 | 14 | 0.1298 | -0.1585 | -0.1222 | 0.1887 | 0.1589 | 0.1811 | 0.4946 | 0.1532 | -0.4042 | -0.0142 | 0.2575 | -0.2456 | 0.2134 | 0.1795 | 0.4338 | 0.2002 | 0.0088 | -0.2627 | 0.2196 | 0.0202 | 0.2831 | 147.1314 | 66.4523 | 18.4789 |
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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 7 through 85 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 86 through 135 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 136 through 158 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 159 through 252 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 253 through 280 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 281 through 300 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 0 through 82 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 83 through 135 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 136 through 158 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 159 through 203 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 204 through 236 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 237 through 252 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 253 through 280 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 281 through 298 ) | | | | | | | | | | | | | |
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