ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.10_2155精密化 | PDB_EXTRACT | 3.25 | データ抽出 | MOSFLM | | 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 開始モデル: 6TCM 解像度: 2.05→28.077 Å / SU ML: 0.23 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 21.33
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2214 | 1409 | 4.96 % |
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Rwork | 0.1735 | - | - |
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obs | 0.1759 | 28385 | 99.67 % |
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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: 79.68 Å2 / Biso mean: 23.8422 Å2 / Biso min: 7.69 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.05→28.077 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3248 | 0 | 6 | 304 | 3558 |
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Biso mean | - | - | 45.81 | 30.69 | - |
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残基数 | - | - | - | - | 434 |
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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_d0.008 | 3370 | X-RAY DIFFRACTION | f_angle_d0.954 | 4608 | X-RAY DIFFRACTION | f_chiral_restr0.056 | 514 | X-RAY DIFFRACTION | f_plane_restr0.006 | 592 | X-RAY DIFFRACTION | f_dihedral_angle_d12.394 | 2000 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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2.05-2.1232 | 0.3015 | 137 | 0.227 | 2575 | 97 | 2.1232-2.2082 | 0.2566 | 135 | 0.2131 | 2664 | 100 | 2.2082-2.3087 | 0.2738 | 143 | 0.1889 | 2675 | 100 | 2.3087-2.4303 | 0.269 | 137 | 0.187 | 2656 | 100 | 2.4303-2.5825 | 0.2627 | 144 | 0.1861 | 2678 | 100 | 2.5825-2.7817 | 0.2243 | 135 | 0.1815 | 2691 | 100 | 2.7817-3.0614 | 0.2405 | 138 | 0.1774 | 2678 | 100 | 3.0614-3.5036 | 0.2096 | 144 | 0.173 | 2713 | 100 | 3.5036-4.4114 | 0.1794 | 148 | 0.1444 | 2770 | 100 | 4.4114-28.077 | 0.1847 | 148 | 0.1591 | 2876 | 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 | 0.5351 | 0.0646 | -0.3025 | 0.3069 | 0.2619 | 0.3227 | 0.1651 | 0.0579 | 0.1056 | -0.0258 | -0.0144 | -0.1788 | -0.2313 | 0.1688 | 0.154 | 0.2458 | 0.0145 | 0.0268 | 0.1622 | 0.0188 | 0.1513 | 14.7141 | 1.9488 | -9.9596 | 2 | 0.1166 | 0.2002 | -0.0322 | 0.233 | -0.0993 | 0.2234 | 0.2326 | 0.4131 | -0.3788 | -0.1513 | -0.3463 | -0.3995 | -0.1931 | 0.12 | -0.0043 | 0.1916 | 0.028 | 0.0187 | 0.3329 | -0.0268 | 0.2759 | 20.1985 | -10.7765 | -9.7671 | 3 | 0.3181 | 0.2314 | -0.3916 | 0.1587 | -0.2689 | 0.3354 | 0.2975 | 0.0376 | 0.0299 | -0.302 | -0.1147 | 0.1212 | -0.2639 | -0.0363 | 0.0214 | 0.1655 | 0.0256 | 0.0067 | 0.1235 | -0.0029 | 0.1152 | 6.4105 | -6.3397 | -7.5826 | 4 | 0.2178 | 0.1999 | 0.1269 | 0.2462 | -0.0476 | 0.3376 | 0.1072 | 0.3651 | -0.4054 | -0.7171 | 0.0965 | 0.3656 | 0.6039 | -0.3581 | 0.0036 | 0.3602 | 0.0682 | -0.102 | 0.2309 | -0.0334 | 0.2065 | 5.5225 | -11.4746 | -17.2182 | 5 | 0.1024 | 0.1958 | 0.3235 | 0.6465 | 0.0659 | 0.9535 | -0.0148 | -0.0835 | -0.1839 | -0.0861 | -0.0195 | 0.1585 | -0.1601 | 0.0959 | 0 | 0.1806 | 0.0089 | 0.0058 | 0.202 | 0.0168 | 0.1502 | 12.1916 | -3.5346 | -16.2359 | 6 | 0.5754 | 0.0124 | -0.0923 | 0.3177 | -0.02 | 0.5697 | 0.0987 | 0.0936 | -0.2516 | -0.0334 | -0.1129 | 0.2818 | 0.0054 | -0.0168 | -0.0104 | 0.0915 | 0.0193 | -0.0117 | 0.1075 | -0.0162 | 0.1408 | 10.3642 | -14.2933 | -4.4395 | 7 | 0.1949 | 0.2602 | -0.0226 | 0.2533 | 0.1629 | 0.0817 | -0.017 | 0.0987 | 0.0402 | -0.1641 | 0.011 | 0.0412 | -0.1409 | 0.0107 | -0 | 0.2333 | -0.003 | -0.0113 | 0.1477 | 0.032 | 0.1933 | 11.6207 | 11.3266 | -7.3401 | 8 | 0.0446 | -0.0538 | -0.059 | 0.4169 | 0.1748 | 0.0807 | -0.2388 | -0.3944 | 0.1022 | 0.0013 | 0.0993 | -0.0925 | -0.6378 | -0.0161 | 0.0325 | 0.2156 | 0.0029 | -0.0689 | 0.3171 | 0.0033 | 0.1873 | 17.2071 | 21.3347 | 12.2845 | 9 | 0.4306 | 0.2613 | -0.5132 | 0.8082 | 0.0267 | 0.6754 | -0.1863 | -0.1963 | -0.0899 | -0.0634 | 0.0017 | -0.0543 | 0.0737 | 0.2418 | -0.1362 | 0.168 | 0.0478 | 0.0227 | 0.2349 | 0.0429 | 0.1559 | 15.8016 | 14.2615 | 10.014 | 10 | 0.2279 | 0.3221 | 0.1725 | 0.8297 | 0.3268 | 1.0718 | -0.2541 | -0.4595 | -0.0897 | -0.3856 | -0.0303 | -0.3197 | -0.3967 | 0.265 | -0.0056 | 0.1041 | 0.0401 | -0.0004 | 0.4006 | 0.0557 | 0.2283 | 24.8204 | 17.5071 | 8.3936 | 11 | 0.8833 | -0.296 | -0.397 | 0.2738 | 0.1899 | 0.2899 | -0.0109 | -0.0747 | -0.1211 | 0.118 | 0.0054 | 0.2978 | -0.1631 | -0.2066 | 0.0504 | 0.158 | 0.0087 | 0.0504 | 0.1588 | 0.0097 | 0.195 | -4.6366 | -10.7952 | 10.6719 | 12 | 1.1932 | -0.1131 | -0.6006 | 0.1854 | 0.0103 | 0.4513 | 0.021 | 0.1564 | -0.1184 | 0.0151 | 0.029 | 0.006 | -0.0031 | 0.0951 | 0.0611 | 0.0813 | -0.0074 | -0.0002 | 0.0988 | -0.0084 | 0.1226 | 3.1023 | -16.0721 | 2.2354 | 13 | 0.241 | -0.1036 | -0.0785 | -0.006 | 0.1273 | 0.7034 | 0.0935 | -0.0784 | -0.1486 | 0.1956 | 0.0438 | -0.0303 | 0.1837 | -0.0221 | 0.0588 | 0.0889 | -0.0029 | -0.0142 | 0.109 | 0.0116 | 0.1588 | 3.9665 | -19.663 | 9.4996 | 14 | 0.2809 | 0.0613 | 0.2065 | 0.7675 | -0.2303 | 0.7563 | 0.0543 | 0.027 | -0.1332 | 0.0252 | 0.1124 | 0.0306 | -0.0583 | 0.0444 | 0.0573 | 0.0849 | 0.011 | 0.0296 | 0.1227 | 0.0039 | 0.1613 | 2.3675 | -11.1512 | 5.5449 | 15 | 0.0659 | -0.0792 | 0.1868 | 0.0684 | 0.0154 | 0.0591 | 0.0705 | -0.0805 | -0.2164 | 0.1479 | 0.0376 | -0.2285 | 0.2555 | 0.2072 | -0.0001 | 0.2085 | -0.014 | 0.0254 | 0.1919 | 0.0123 | 0.1217 | 1.6608 | 1.7736 | 22.066 | 16 | 0.2755 | 0.1448 | -0.3614 | 0.6973 | -0.0367 | 1.3623 | -0.0058 | -0.2989 | 0.1167 | 0.0665 | 0.0577 | -0.0405 | -0.3448 | 0.1285 | 0.0739 | 0.2506 | -0.0306 | -0.0309 | 0.186 | -0.0099 | 0.1636 | 8.3107 | 22.6283 | 16.8431 | 17 | 0.9311 | 1.0187 | -0.5368 | 0.753 | -0.591 | 0.4382 | -0.0224 | -0.0182 | 0.025 | 0.0095 | -0.0993 | -0.1968 | 0.0055 | -0.0842 | -0.0017 | 0.2279 | 0.0403 | 0.0012 | 0.1777 | -0.0178 | 0.1399 | 4.1617 | 15.5014 | 16.2585 | 18 | 1.045 | -0.6445 | -0.1091 | 0.591 | -0.1968 | 0.5288 | -0.0613 | -0.2557 | 0.2595 | 0.2208 | 0.0848 | 0.0713 | -0.4715 | 0.0879 | 0.0142 | 0.3432 | -0.0178 | -0.0423 | 0.1532 | -0.0506 | 0.166 | 5.5345 | 28.51 | 19.5457 |
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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 'H' and (resid 1 through 17 )H1 - 17 | 2 | X-RAY DIFFRACTION | 2 | chain 'H' and (resid 18 through 33 )H18 - 33 | 3 | X-RAY DIFFRACTION | 3 | chain 'H' and (resid 34 through 52 )H34 - 52 | 4 | X-RAY DIFFRACTION | 4 | chain 'H' and (resid 53 through 67 )H53 - 67 | 5 | X-RAY DIFFRACTION | 5 | chain 'H' and (resid 68 through 91 )H68 - 91 | 6 | X-RAY DIFFRACTION | 6 | chain 'H' and (resid 92 through 111 )H92 - 111 | 7 | X-RAY DIFFRACTION | 7 | chain 'H' and (resid 112 through 127 )H112 - 127 | 8 | X-RAY DIFFRACTION | 8 | chain 'H' and (resid 128 through 153 )H128 - 153 | 9 | X-RAY DIFFRACTION | 9 | chain 'H' and (resid 154 through 197 )H154 - 197 | 10 | X-RAY DIFFRACTION | 10 | chain 'H' and (resid 198 through 222 )H198 - 222 | 11 | X-RAY DIFFRACTION | 11 | chain 'L' and (resid 1 through 25 )L1 - 25 | 12 | X-RAY DIFFRACTION | 12 | chain 'L' and (resid 26 through 52 )L26 - 52 | 13 | X-RAY DIFFRACTION | 13 | chain 'L' and (resid 53 through 79 )L | | | | | | | | | | | | | | | | | | | | | | | | | |
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