ソフトウェア | 名称 | バージョン | 分類 |
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Aimless | 0.3.11データスケーリング | PHASER | 2.5.6位相決定 | PHENIX | 1.12_2829精密化 | PDB_EXTRACT | 3.25 | 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: 4BZ3 解像度: 1.636→29.139 Å / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 17.69 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1812 | 1993 | 4.01 % |
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Rwork | 0.1605 | 47649 | - |
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obs | 0.1614 | 49642 | 96.84 % |
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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: 56.47 Å2 / Biso mean: 20.1999 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: 1.636→29.139 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3451 | 0 | 96 | 378 | 3925 |
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Biso mean | - | - | 17.94 | 28.97 | - |
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残基数 | - | - | - | - | 465 |
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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 | 3686 | X-RAY DIFFRACTION | f_angle_d0.719 | 5061 | X-RAY DIFFRACTION | f_chiral_restr0.049 | 574 | X-RAY DIFFRACTION | f_plane_restr0.005 | 668 | X-RAY DIFFRACTION | f_dihedral_angle_d9.886 | 2141 | | | | | |
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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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1.6365-1.6774 | 0.2977 | 132 | 0.26 | 3146 | 90 | 1.6774-1.7228 | 0.2448 | 148 | 0.2317 | 3467 | 99 | 1.7228-1.7734 | 0.2498 | 141 | 0.2092 | 3466 | 99 | 1.7734-1.8307 | 0.208 | 144 | 0.1964 | 3435 | 98 | 1.8307-1.8961 | 0.2225 | 141 | 0.1865 | 3424 | 98 | 1.8961-1.972 | 0.2183 | 141 | 0.181 | 3436 | 97 | 1.972-2.0617 | 0.2056 | 137 | 0.1589 | 3255 | 94 | 2.0617-2.1704 | 0.1748 | 152 | 0.1466 | 3454 | 98 | 2.1704-2.3063 | 0.1955 | 140 | 0.145 | 3487 | 99 | 2.3063-2.4843 | 0.1604 | 149 | 0.1404 | 3472 | 99 | 2.4843-2.7341 | 0.151 | 146 | 0.1413 | 3463 | 98 | 2.7341-3.1294 | 0.1722 | 146 | 0.1443 | 3446 | 98 | 3.1294-3.9411 | 0.144 | 137 | 0.1369 | 3266 | 93 | 3.9411-29.1 | 0.1684 | 139 | 0.1647 | 3432 | 95 |
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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 | 2.6573 | -0.2583 | 0.6102 | 1.6126 | -0.5271 | 1.8115 | -0.0343 | 0.0373 | 0.083 | -0.0676 | 0.0189 | 0.0607 | -0.0153 | -0.0929 | -0.0086 | 0.1133 | -0.0003 | 0.003 | 0.1004 | 0.0054 | 0.1013 | -41.3409 | 22.6921 | 72.2345 | 2 | 3.5636 | -0.3986 | 1.1792 | 1.8953 | -0.8564 | 3.0085 | -0.0249 | -0.0156 | 0.2052 | 0.0548 | -0.0061 | -0.0934 | -0.1532 | 0.0793 | 0.0739 | 0.1405 | -0.0092 | -0.0009 | 0.1003 | -0.015 | 0.1235 | -36.0364 | 29.016 | 74.8212 | 3 | 0.8073 | -0.094 | 0.2806 | 2.5458 | -2.3425 | 2.4319 | 0.0474 | -0.1163 | 0.1075 | 0.416 | 0.0082 | -0.0724 | -0.5623 | 0.1032 | -0.066 | 0.2011 | -0.0075 | 0.0005 | 0.1402 | -0.0185 | 0.1397 | -36.5668 | 26.613 | 82.766 | 4 | 1.3484 | 0.148 | 0.7361 | 1.7131 | -0.4273 | 1.2732 | 0.0003 | -0.1242 | -0.0817 | 0.0967 | 0.0117 | 0.0466 | -0.0545 | -0.0518 | -0.0016 | 0.1148 | -0.0058 | 0.0241 | 0.1015 | 0.004 | 0.0971 | -38.7397 | 13.3303 | 80.8569 | 5 | 9.818 | -0.6673 | -2.9006 | 1.8451 | 0.2781 | 3.6646 | -0.0694 | -0.5553 | -0.2605 | 0.1952 | 0.0592 | 0.0733 | 0.0472 | -0.1002 | 0.0674 | 0.1317 | -0.0043 | -0.0121 | 0.1497 | 0.0254 | 0.107 | -34.6057 | 9.142 | 89.1196 | 6 | 2.3127 | -0.2564 | -1.3579 | 1.7612 | 0.1285 | 5.5488 | 0.069 | -0.0386 | -0.0643 | 0.0778 | 0.0412 | 0.3176 | 0.2467 | -0.3679 | -0.0911 | 0.1213 | -0.0153 | 0.0113 | 0.1331 | 0.0183 | 0.1586 | -45.4157 | 7.1071 | 79.6762 | 7 | 6.7817 | -0.7592 | 0.4986 | 1.5652 | 0.2229 | 1.4495 | -0.015 | -0.1312 | -0.1436 | 0.0862 | 0.007 | 0.0523 | 0.0818 | -0.0009 | 0.0182 | 0.1566 | 0.0027 | -0.004 | 0.1166 | 0.0139 | 0.1201 | -30.9453 | 1.5498 | 82.377 | 8 | 3.8576 | 0.5882 | -1.4828 | 2.3514 | 1.3749 | 2.6859 | -0.2151 | 0.1572 | 0.6528 | 0.0321 | 0.1251 | 0.7349 | -0.6081 | -0.6956 | 0.0569 | 0.2597 | 0.0837 | -0.0521 | 0.2899 | 0.0158 | 0.3153 | -33.9295 | 3.722 | 50.0792 | 9 | 2.2429 | -0.52 | -0.7015 | 2.6563 | 0.8293 | 3.1713 | -0.1203 | 0.1324 | -0.0357 | -0.1407 | -0.0371 | 0.1536 | 0.1233 | -0.128 | 0.1297 | 0.1099 | -0.0041 | -0.0201 | 0.1073 | 0.0062 | 0.1218 | -26.7435 | -4.3225 | 47.5741 | 10 | 2.7529 | 0.3019 | 0.3114 | 3.4236 | -1.5 | 8.7596 | -0.0356 | 0.0325 | 0.1805 | -0.2942 | -0.019 | 0.5162 | -0.0603 | -0.7507 | 0.0616 | 0.1318 | 0.0045 | -0.0597 | 0.1811 | -0.0332 | 0.2125 | -34.9018 | -9.2152 | 45.6805 | 11 | 1.6455 | 0.4188 | 1.2624 | 1.3948 | 0.615 | 2.6843 | -0.0044 | 0.0924 | -0.0116 | 0.0003 | -0.0008 | 0.0976 | 0.0791 | -0.019 | 0.0183 | 0.1311 | -0.0133 | 0.01 | 0.0971 | -0 | 0.1276 | -23.6778 | -11.3909 | 50.8703 | 12 | 3.5085 | 0.5275 | 1.0698 | 1.6012 | 1.0049 | 3.6365 | 0.0604 | -0.1849 | -0.122 | 0.2417 | -0.0266 | 0.0307 | 0.2875 | -0.038 | -0.0598 | 0.2004 | 0.0003 | 0.0115 | 0.0959 | 0.0036 | 0.1536 | -21.3869 | -17.8367 | 56.6955 | 13 | 0.833 | 0.1927 | 0.2582 | 1.7963 | 0.2741 | 0.8279 | 0.002 | 0.0334 | -0.0387 | -0.033 | 0.0149 | -0.0563 | 0.0159 | 0.0873 | -0.0038 | 0.1103 | 0.0014 | 0.0129 | 0.1288 | -0.0033 | 0.1131 | -14.2235 | -5.4745 | 53.7373 | 14 | 3.6 | -0.3849 | -2.435 | 2.7617 | 0.9507 | 1.9642 | 0.0221 | -0.1138 | 0.0527 | -0.1115 | 0.0649 | -0.3193 | -0.1079 | 0.257 | -0.0485 | 0.1027 | -0.0116 | 0.0017 | 0.1377 | -0.0071 | 0.1155 | -5.4479 | 1.2421 | 56.3322 | 15 | 5.8737 | -0.4596 | -2.4048 | 1.5889 | 0.8173 | 2.7297 | 0.0374 | 0.3022 | 0.3336 | -0.4042 | -0.0153 | -0.0287 | -0.205 | 0.0236 | -0.0196 | 0.1686 | -0.0167 | -0.0083 | 0.1137 | 0.0244 | 0.1074 | -16.0944 | 3.6248 | 46.5835 | 16 | 2.2012 | 0.1462 | 0.7813 | 2.0003 | 0.3501 | 7.5391 | -0.0729 | -0.0279 | 0.1603 | -0.0342 | 0.0426 | -0.0015 | -0.2269 | 0.1645 | 0.0347 | 0.1151 | -0.0081 | 0.0026 | 0.1096 | -0.0148 | 0.1575 | -11.5069 | 9.4898 | 59.906 | 17 | 3.5463 | 0.8011 | -0.4178 | 2.0843 | -0.3931 | 0.9579 | -0.0129 | 0.6844 | -0.553 | -0.3503 | -0.035 | 0.0635 | 0.2475 | -0.3216 | 0.0255 | 0.2283 | -0.0119 | -0.0388 | 0.2622 | -0.0636 | 0.2467 | -47.6035 | 9.2523 | 64.3225 | 18 | 4.3567 | -1.3716 | -1.5628 | 2.4134 | 0.7395 | 2.0422 | 0.1308 | 0.0053 | 0.1247 | -0.1604 | -0.0083 | -0.0403 | -0.1248 | 0.0684 | -0.1006 | 0.132 | 0.0038 | -0.0088 | 0.1261 | -0.0033 | 0.1277 | -42.2188 | 14.1618 | 67.8542 | 19 | 2.9673 | 0.2749 | -0.5075 | 1.4168 | -0.2777 | 2.107 | 0.0523 | -0.0378 | 0.2058 | 0.0061 | 0.029 | 0.0852 | -0.0826 | -0.0185 | -0.0985 | 0.1239 | 0.0002 | 0.0012 | 0.1284 | -0.0007 | 0.1619 | -46.1784 | 21.8579 | 71.4215 | 20 | 1.3783 | 0.9899 | -1.0251 | 2.8562 | -0.4434 | 3.6903 | -0.1171 | 0.3666 | 0.1132 | -0.5582 | 0.1456 | 0.4036 | 0.2825 | -0.3568 | -0.0276 | 0.1645 | 0.0045 | -0.0497 | 0.1612 | 0.0127 | 0.1534 | -48.2151 | 21.5347 | 61.8161 |
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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 'B' and (resid 103 through 122 )B103 - 122 | 2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 123 through 146 )B123 - 146 | 3 | X-RAY DIFFRACTION | 3 | chain 'B' and (resid 147 through 163 )B147 - 163 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 164 through 215 )B164 - 215 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 216 through 229 )B216 - 229 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 230 through 245 )B230 - 245 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 246 through 263 )B246 - 263 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 32 through 44 )A32 - 44 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 45 through 88 )A45 - 88 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 89 through 102 )A89 - 102 | 11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 103 through 122 )A103 - 122 | 12 | X-RAY DIFFRACTION | 12 | chain 'A' and (resid 123 through 146 )A123 - 146 | 13 | X-RAY DIFFRACTION | 13 | chain 'A' and (resid 147 through 215 )A | | | | | | | | | | | | | | | | | | | | | | | | | |
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