ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.8.4_1496精密化 | PHASER | 2.7.16位相決定 | Aimless | 0.5.23データスケーリング | PDB_EXTRACT | 3.22 | データ抽出 | XDS | | データ削減 | | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5dtk 解像度: 1.796→44.261 Å / SU ML: 0.27 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.43 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2268 | 4637 | 4.89 % |
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Rwork | 0.1834 | 90113 | - |
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obs | 0.1855 | 94750 | 95.91 % |
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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 max: 88.53 Å2 / Biso mean: 21.73 Å2 / Biso min: 7.93 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.796→44.261 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7868 | 0 | 71 | 1111 | 9050 |
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Biso mean | - | - | 24.62 | 31.29 | - |
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残基数 | - | - | - | - | 956 |
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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_d0.01 | 8252 | X-RAY DIFFRACTION | f_angle_d1.099 | 11207 | X-RAY DIFFRACTION | f_chiral_restr0.05 | 1192 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1448 | X-RAY DIFFRACTION | f_dihedral_angle_d11.959 | 2990 | | | | | |
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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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1.7965-1.8169 | 0.4447 | 147 | 0.4138 | 2761 | X-RAY DIFFRACTION | 88 | 1.8169-1.8383 | 0.3958 | 159 | 0.3973 | 2949 | X-RAY DIFFRACTION | 96 | 1.8383-1.8607 | 0.4242 | 167 | 0.3665 | 3016 | X-RAY DIFFRACTION | 96 | 1.8607-1.8843 | 0.377 | 137 | 0.3427 | 2998 | X-RAY DIFFRACTION | 96 | 1.8843-1.909 | 0.3094 | 165 | 0.3122 | 2968 | X-RAY DIFFRACTION | 96 | 1.909-1.9352 | 0.3833 | 164 | 0.3111 | 2939 | X-RAY DIFFRACTION | 95 | 1.9352-1.9628 | 0.3608 | 156 | 0.3155 | 2894 | X-RAY DIFFRACTION | 92 | 1.9628-1.9921 | 0.2675 | 159 | 0.2354 | 3022 | X-RAY DIFFRACTION | 96 | 1.9921-2.0233 | 0.2498 | 159 | 0.2067 | 3007 | X-RAY DIFFRACTION | 97 | 2.0233-2.0564 | 0.2178 | 160 | 0.1912 | 3009 | X-RAY DIFFRACTION | 97 | 2.0564-2.0919 | 0.272 | 182 | 0.2231 | 2941 | X-RAY DIFFRACTION | 95 | 2.0919-2.1299 | 0.2875 | 143 | 0.2418 | 2882 | X-RAY DIFFRACTION | 93 | 2.1299-2.1709 | 0.2393 | 172 | 0.1912 | 2996 | X-RAY DIFFRACTION | 97 | 2.1709-2.2152 | 0.2338 | 175 | 0.1805 | 3035 | X-RAY DIFFRACTION | 97 | 2.2152-2.2634 | 0.2335 | 146 | 0.1817 | 3037 | X-RAY DIFFRACTION | 96 | 2.2634-2.316 | 0.2929 | 113 | 0.211 | 2852 | X-RAY DIFFRACTION | 90 | 2.316-2.3739 | 0.1962 | 166 | 0.1671 | 3009 | X-RAY DIFFRACTION | 97 | 2.3739-2.4381 | 0.2019 | 157 | 0.1618 | 3079 | X-RAY DIFFRACTION | 98 | 2.4381-2.5099 | 0.1995 | 158 | 0.1623 | 3020 | X-RAY DIFFRACTION | 97 | 2.5099-2.5909 | 0.2063 | 151 | 0.1569 | 3087 | X-RAY DIFFRACTION | 98 | 2.5909-2.6835 | 0.224 | 137 | 0.1616 | 3082 | X-RAY DIFFRACTION | 98 | 2.6835-2.7909 | 0.2051 | 144 | 0.163 | 3012 | X-RAY DIFFRACTION | 96 | 2.7909-2.9179 | 0.1832 | 156 | 0.1609 | 3078 | X-RAY DIFFRACTION | 98 | 2.9179-3.0717 | 0.2252 | 167 | 0.1673 | 3079 | X-RAY DIFFRACTION | 98 | 3.0717-3.2641 | 0.1959 | 124 | 0.1697 | 3101 | X-RAY DIFFRACTION | 98 | 3.2641-3.516 | 0.2118 | 152 | 0.162 | 2999 | X-RAY DIFFRACTION | 96 | 3.516-3.8696 | 0.1766 | 144 | 0.1463 | 3052 | X-RAY DIFFRACTION | 96 | 3.8696-4.4291 | 0.1902 | 153 | 0.1373 | 2974 | X-RAY DIFFRACTION | 94 | 4.4291-5.5785 | 0.1594 | 112 | 0.1315 | 3116 | X-RAY DIFFRACTION | 97 | 5.5785-44.261 | 0.1952 | 212 | 0.1603 | 3119 | X-RAY DIFFRACTION | 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 | 0.1354 | 0.017 | 0.0023 | 0.0888 | 0.0086 | 0.0106 | -0.0993 | -0.1179 | -0.4057 | 0.0499 | 0.2419 | -0.0889 | 0.0333 | -0.0751 | 0.0045 | 0.2768 | -0.0337 | -0.0065 | 0.2361 | 0.1093 | 0.3618 | -30.847 | -24.079 | 13.257 | 2 | 0.1281 | -0.0055 | 0.1412 | 0.2102 | 0.1097 | 0.3862 | -0.0305 | 0.0452 | -0.1833 | 0.0125 | -0.0138 | 0.1858 | 0.0297 | -0.2029 | -0.0763 | 0.1023 | -0.0141 | 0.0175 | 0.1276 | 0.0174 | 0.2507 | -30.255 | -15.397 | 0.823 | 3 | 0.0441 | 0.0294 | 0.0156 | 0.0617 | -0.0365 | 0.0575 | 0.1104 | -0.0203 | 0.2207 | 0.0338 | 0.0741 | 0.0697 | -0.0282 | -0.0977 | 0.0006 | 0.1821 | 0.045 | 0.0396 | 0.1681 | -0.0075 | 0.2079 | -22.949 | 10.243 | -4.017 | 4 | 0.0316 | -0.0074 | -0.0384 | 0.0067 | 0.0084 | 0.0457 | 0.1113 | -0.0354 | 0.1576 | 0.059 | -0.0279 | 0.0647 | -0.0307 | -0.0432 | 0.0097 | 0.1768 | 0.0222 | 0.0247 | 0.1533 | -0.0242 | 0.1535 | -21.018 | 5.851 | 2.173 | 5 | 0.1291 | 0.0238 | -0.0953 | 0.0393 | -0.0315 | 0.1783 | 0.0481 | 0.13 | 0.1481 | 0.0136 | 0.0179 | 0.0499 | -0.1113 | -0.2099 | 0.0386 | 0.1201 | 0.0441 | -0.0259 | 0.2048 | 0.0477 | 0.1756 | -32.904 | 0.45 | -11.329 | 6 | 0.1282 | -0.0905 | 0.0268 | 0.0715 | -0.0859 | 0.2915 | 0.0512 | 0.1573 | -0.0687 | -0.0798 | -0.068 | 0.1261 | -0.0207 | -0.1178 | -0.0179 | 0.1331 | 0.0166 | -0.0291 | 0.1608 | -0.0092 | 0.1711 | -29.59 | -8.768 | -7.756 | 7 | 0.0904 | 0.0754 | 0.0466 | 0.1193 | -0.0441 | 0.1322 | -0.0354 | -0.0131 | -0.0104 | 0.0312 | -0.0025 | 0.1154 | 0.0732 | -0.0354 | -0.0085 | 0.1037 | 0.0006 | -0.0012 | 0.1392 | 0.0065 | 0.1553 | -22.55 | -10.948 | 4.112 | 8 | 0.0409 | 0.024 | 0.0251 | 0.0205 | -0.0061 | 0.0714 | -0.0427 | -0.247 | -0.1314 | 0.0895 | 0.0158 | 0.1984 | -0.0885 | -0.0326 | 0.0001 | 0.1752 | 0.0035 | 0.0262 | 0.2179 | 0.0168 | 0.1553 | -24.409 | -15.415 | 10.931 | 9 | 0.1378 | -0.0009 | -0.035 | 0 | 0.0006 | 0.0097 | 0.0516 | -0.2083 | 0.1004 | 0.1734 | -0.0393 | -0.0879 | 0.0733 | -0.0338 | 0.294 | 0.3473 | -0.0262 | -0.1912 | 0.4098 | -0.1373 | 0.2761 | 13.293 | 3.902 | 10.124 | 10 | 0.2888 | -0.1463 | -0.1675 | 0.2656 | -0.0204 | 0.1352 | 0.0096 | -0.0677 | 0.043 | -0.0013 | 0.0282 | -0.2673 | 0.0417 | 0.0752 | -0.0665 | 0.1124 | -0.0017 | -0.028 | 0.0962 | -0.029 | 0.1812 | 9.004 | -0.809 | -3.85 | 11 | 0.076 | 0.072 | -0.0125 | 0.0674 | 0.0085 | 0.1076 | 0.1193 | -0.1142 | -0.0445 | -0.1558 | 0.0241 | -0.026 | 0.2598 | 0.033 | 0.0214 | 0.2287 | 0.03 | -0.0144 | 0.1141 | 0.032 | 0.151 | -0.555 | -24.448 | -12.45 | 12 | 0.317 | -0.022 | -0.0722 | 0.0948 | 0.0488 | 0.0381 | 0.1011 | -0.1154 | 0.058 | -0.0851 | -0.1081 | -0.0325 | 0.1871 | -0.0081 | 0.0093 | 0.1497 | -0.0006 | -0.017 | 0.0946 | 0.0402 | 0.1185 | -0.169 | -21.856 | -5.109 | 13 | 0.063 | -0.0091 | 0.0433 | 0.0284 | -0.0057 | 0.0455 | 0.0021 | -0.0155 | -0.0243 | -0.0401 | 0.0234 | -0.0409 | -0.0009 | 0.089 | 0.0058 | 0.1605 | 0.0033 | 0.0234 | 0.1112 | -0.008 | 0.1265 | 6.937 | -13.885 | -19.447 | 14 | 0.2387 | -0.0879 | 0.0433 | 0.6629 | 0.0548 | 0.1629 | 0.0224 | -0.056 | 0.0379 | 0.0307 | 0.002 | -0.1556 | -0.0203 | 0.0107 | -0.0042 | 0.1123 | 0.0053 | -0.0097 | 0.1004 | -0.004 | 0.1173 | 4.883 | -5.233 | -6.196 | 15 | 0.7306 | 0.3731 | -0.0384 | 0.7376 | 0.0184 | 0.4764 | 0.0552 | -0.2443 | -0.0778 | 0.2123 | 0.0024 | -0.153 | 0.0515 | 0.0815 | -0.1303 | 0.2911 | 0.0328 | -0.0883 | 0.2891 | -0.032 | 0.103 | 5.077 | -3.65 | 10.184 | 16 | 0.5954 | 0.008 | 0.3291 | 0.0441 | 0.0904 | 0.3536 | 0.0867 | 0.1168 | -0.2591 | -0.111 | 0.0283 | -0.0263 | -0.0374 | 0.033 | 0.5499 | 0.2768 | 0.0289 | 0.1686 | 0.1884 | -0.0875 | 0.4147 | 0.212 | -8.421 | 36.394 | 17 | 0.2934 | 0.2506 | -0.1559 | 0.2189 | -0.1111 | 0.2036 | -0.0719 | -0.0065 | -0.1381 | 0.0329 | 0.0199 | -0.2001 | 0.017 | 0.0819 | -0.0891 | 0.1177 | 0.0027 | 0.0024 | 0.1129 | 0.0102 | 0.2137 | -4.493 | 3.141 | 46.596 | 18 | 0.0645 | 0.0722 | -0.0297 | 0.1025 | 0.0242 | 0.1333 | 0.0537 | 0.0486 | 0.0408 | -0.051 | 0.0466 | 0.0843 | -0.0274 | 0.0063 | 0.0447 | 0.1425 | -0.0124 | 0.0127 | 0.1196 | 0.0411 | 0.1374 | -13.814 | 24.377 | 38.799 | 19 | 0.1655 | 0.0198 | -0.0224 | 0.0178 | 0.0377 | 0.1053 | 0.1178 | -0.0942 | 0.1105 | 0.1218 | 0.0161 | 0.0022 | -0.1319 | 0.0383 | 0.0394 | 0.1823 | -0.0405 | -0.0053 | 0.1555 | -0.0063 | 0.1391 | -6.534 | 22.176 | 53.313 | 20 | 0.3276 | 0.1374 | -0.1575 | 0.5797 | -0.0011 | 0.0869 | -0.0073 | 0.0173 | -0.1416 | 0.0084 | 0.0001 | -0.1004 | -0.0088 | 0.0162 | 0.0001 | 0.1125 | -0.0104 | -0.003 | 0.1069 | 0.0071 | 0.1209 | -8.46 | 7.613 | 46.248 | 21 | 0.0253 | -0.0238 | -0.0004 | 0.0609 | 0.0445 | 0.0483 | 0.0433 | 0.1883 | -0.1046 | -0.1454 | -0.0757 | -0.0274 | -0.0502 | -0.051 | 0.0049 | 0.2051 | -0.028 | 0.0302 | 0.2007 | -0.0558 | 0.1796 | -8.143 | -1.96 | 32.765 | 22 | 0.0341 | 0.0026 | -0.0107 | 0.0228 | 0.0158 | 0.0359 | -0.056 | 0.2912 | 0.1656 | -0.0699 | 0.021 | -0.0057 | -0.0126 | -0.0999 | 0.0001 | 0.2671 | -0.0281 | -0.0207 | 0.4711 | 0.0305 | 0.1946 | -42.738 | 13.045 | 19.08 | 23 | 0.186 | 0.0216 | 0.0944 | 0.0887 | 0.0396 | 0.1389 | -0.0267 | 0.2721 | 0.1222 | -0.0378 | 0.0113 | -0.0628 | -0.1322 | -0.1117 | -0.0055 | 0.1835 | -0.0011 | -0.0343 | 0.2594 | 0.0613 | 0.1723 | -41.026 | 17.349 | 27.031 | 24 | 0.1759 | 0.0254 | -0.0549 | 0.1333 | -0.0544 | 0.0322 | -0.0259 | 0.1024 | 0.0443 | 0.0232 | 0.0911 | 0.1018 | -0.0609 | -0.1449 | -0.0025 | 0.1119 | 0.0129 | 0.008 | 0.1504 | 0.0415 | 0.1142 | -45.371 | 8.088 | 41.416 | 25 | 0.1842 | -0.1761 | 0.0275 | 0.1669 | -0.0439 | 0.1213 | 0.0161 | 0.083 | -0.1206 | 0.0474 | -0.0048 | 0.0674 | -0.0182 | -0.0791 | 0.0003 | 0.1423 | -0.0087 | -0.0046 | 0.1227 | 0.0015 | 0.1687 | -35.195 | -6.884 | 48.263 | 26 | 0.1085 | -0.0213 | 0.0409 | 0.0712 | -0.0018 | 0.1098 | 0.0353 | -0.0888 | -0.0351 | 0.0199 | -0.0035 | -0.0253 | 0.0989 | -0.1728 | 0.0124 | 0.1211 | -0.0019 | -0.0013 | 0.1756 | 0.0188 | 0.1244 | -46.46 | 3.477 | 53.214 | 27 | 0.1761 | 0.0208 | -0.0619 | 0.0096 | 0.049 | 0.3274 | 0.0469 | -0.0311 | 0.0545 | 0.0607 | -0.0082 | 0.0321 | -0.0301 | -0.0942 | 0 | 0.1132 | 0.0015 | 0.0015 | 0.1355 | 0.0282 | 0.118 | -43.075 | 11.302 | 45.341 | 28 | 0.1218 | -0.0895 | -0.1205 | 0.0832 | 0.1323 | 0.216 | -0.1048 | 0.1773 | 0.0091 | -0.0893 | 0.0685 | 0.0609 | 0.0465 | -0.0948 | -0.0154 | 0.1131 | -0.0222 | -0.0048 | 0.1837 | 0.0038 | 0.1114 | -35.753 | 6.973 | 34.091 | 29 | 0.0554 | -0.0558 | 0.0264 | 0.0588 | -0.0427 | 0.0787 | 0.0591 | 0.2894 | -0.0066 | 0.0473 | -0.0451 | -0.0124 | 0.0783 | -0.0542 | -0.0166 | 0.1533 | -0.021 | -0.0064 | 0.2139 | 0.0201 | 0.1241 | -40.723 | 8.712 | 29.627 | 30 | 0.0623 | -0.0444 | 0.0421 | 0.0498 | 0.0016 | 0.0817 | 0.021 | 0.2396 | 0.0715 | 0.0708 | -0.037 | 0.0398 | 0.1028 | 0.1585 | -0.0255 | 0.1706 | -0.022 | 0.0028 | 0.3383 | -0.0127 | 0.1211 | -34.916 | 6.715 | 23.904 |
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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 25:38 )A25 - 38 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 39:82 )A39 - 82 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 83:102 )A83 - 102 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 103:119 )A103 - 119 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN A AND RESID 120:142 )A120 - 142 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN A AND RESID 143:194 )A143 - 194 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN A AND RESID 195:231 )A195 - 231 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN A AND RESID 232:265 )A232 - 265 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN B AND RESID 25:38 )B25 - 38 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN B AND RESID 39:82 )B39 - 82 | 11 | X-RAY DIFFRACTION | 11 | ( CHAIN B AND RESID 83:102 )B83 - 102 | 12 | X-RAY DIFFRACTION | 12 | ( CHAIN B AND RESID 103:119 )B103 - 119 | 13 | X-RAY DIFFRACTION | 13 | ( CHAIN B AND RESID 120:142 )B120 - 142 | 14 | X-RAY DIFFRACTION | 14 | ( CHAIN B AND RESID 143:243 )B143 - 243 | 15 | X-RAY DIFFRACTION | 15 | ( CHAIN B AND | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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