ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.12_2829精密化 | CrystalClear | | データ収集 | SCALA | | データスケーリング | PDB_EXTRACT | 3.22 | データ抽出 | iMOSFLM | | データ削減 | 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: 6AMJ 解像度: 2.8→35.35 Å / SU ML: 0.41 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 29.97 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.3025 | 1266 | 10 % |
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Rwork | 0.2467 | 11397 | - |
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obs | 0.2522 | 12663 | 99.96 % |
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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: 155.51 Å2 / Biso mean: 60.7622 Å2 / Biso min: 8.67 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.8→35.35 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3209 | 0 | 0 | 0 | 3209 |
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残基数 | - | - | - | - | 425 |
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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_d0.007 | 3284 | X-RAY DIFFRACTION | f_angle_d0.809 | 4469 | X-RAY DIFFRACTION | f_chiral_restr0.047 | 508 | X-RAY DIFFRACTION | f_plane_restr0.005 | 570 | X-RAY DIFFRACTION | f_dihedral_angle_d9.662 | 1941 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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2.8-2.9121 | 0.3913 | 139 | 0.3145 | 1258 | 1397 | 2.9121-3.0445 | 0.3259 | 139 | 0.2873 | 1241 | 1380 | 3.0445-3.2049 | 0.3339 | 141 | 0.2705 | 1266 | 1407 | 3.2049-3.4056 | 0.3152 | 138 | 0.2585 | 1255 | 1393 | 3.4056-3.6683 | 0.3148 | 141 | 0.2651 | 1267 | 1408 | 3.6683-4.037 | 0.3633 | 140 | 0.2773 | 1249 | 1389 | 4.037-4.62 | 0.2681 | 141 | 0.2176 | 1280 | 1421 | 4.62-5.8165 | 0.2557 | 142 | 0.2062 | 1275 | 1417 | 5.8165-35.3527 | 0.2562 | 145 | 0.2158 | 1306 | 1451 |
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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 | 1.3716 | -1.643 | -0.2374 | 1.9641 | 0.2847 | 0.0399 | 0.0201 | -0.6987 | 0.2778 | 0.124 | 0.4196 | -1.4473 | -0.1033 | 1.1375 | -0.2845 | 0.588 | 0.2004 | 0.0052 | 1.5701 | -0.0503 | 0.981 | -12.3078 | -12.0179 | -34.537 | 2 | 1.8715 | -0.3217 | -0.0301 | 2.1398 | 0.4528 | 0.9774 | 0.1207 | 0.2258 | 0.1835 | -0.0174 | -0.2444 | -0.3104 | -0.0107 | 0.1621 | -0.0285 | 0.205 | 0.0937 | -0.0198 | -0.1093 | 0.0144 | 0.1514 | -41.0796 | 2.3192 | -28.5822 | 3 | 1.7372 | 0.4857 | 0.4048 | 3.9139 | 1.4456 | 1.4089 | -0.2957 | -0.1592 | 0.0858 | 0.4895 | -0.1161 | -0.1027 | -0.0334 | 0.032 | -0.1829 | 0.183 | -0.1358 | -0.1866 | -0.2602 | -0.1004 | 0.2347 | -38.1401 | 0.2309 | -24.0645 | 4 | 0.8601 | 0.1057 | -0.3 | 1.262 | -0.0769 | 1.7894 | -0.0592 | 0.0469 | 0.5088 | 0.0052 | -0.0018 | 0.2347 | -0.5324 | 0.0604 | -0.1673 | 0.2933 | -0.013 | -0.0814 | -0.3035 | 0.1126 | 0.3197 | -41.7237 | 11.7443 | -25.4571 | 5 | 1.4115 | 0.8024 | -0.7032 | 0.8515 | -0.1582 | 0.5083 | 0.2845 | -0.1154 | -0.6295 | 0.0571 | -0.5436 | -0.2378 | 1.4222 | 1.0583 | -0.0198 | 1.0105 | 0.4248 | -0.1462 | 0.946 | 0.0281 | 0.6431 | -19.1344 | -20.2272 | -14.8342 | 6 | 0.5185 | 0.6771 | -0.5075 | 0.8911 | -0.6652 | 0.4919 | 0.0119 | -0.1389 | -0.4447 | -0.2835 | -0.3117 | -0.4324 | 1.0052 | 1.0042 | -0.4953 | 1.1717 | 0.7261 | -0.2885 | 1.4011 | -0.0741 | 0.7378 | -12.8032 | -23.8069 | -21.0617 | 7 | 1.2415 | 0.1406 | 0.2756 | 2.8072 | -0.4269 | 0.1367 | 0.0408 | 0.217 | -0.4826 | -0.0393 | 0.0856 | -1.1437 | 0.4572 | 1.1727 | -0.2623 | 0.6626 | 0.3233 | -0.1058 | 1.5599 | -0.0475 | 0.6824 | -8.0382 | -12.7497 | -21.3837 | 8 | 4.029 | 0.07 | 1.5169 | 3.849 | -0.4449 | 1.513 | 0.2415 | -0.5415 | -0.5462 | 0.246 | -0.125 | -0.6589 | 0.5357 | 0.5514 | -0.4883 | 0.835 | 0.622 | -0.0717 | 1.1861 | 0.1462 | 0.8405 | -12.3751 | -17.3768 | -15.9162 | 9 | 3.1183 | -0.0575 | 0.4008 | 1.8 | -0.0933 | 3.5044 | -0.1643 | 0.5185 | -0.7824 | -0.139 | -0.2921 | -0.2145 | 0.6206 | 0.5805 | 0.0667 | 0.911 | 0.7139 | 0.1832 | 1.3977 | 0.2109 | 0.9671 | -14.5875 | -24.8627 | -29.6777 | 10 | 6.4394 | -0.6502 | -1.3395 | 1.417 | 0.0977 | 0.279 | 0.1699 | -0.4726 | -0.3287 | 0.2539 | -0.4133 | -0.3741 | 0.4326 | 0.4458 | 0.1794 | 0.2 | 0.0456 | -0.165 | 0.5004 | 0.0109 | 0.1883 | -28.2831 | -9.0779 | -7.5052 | 11 | 2.6179 | 0.1894 | 0.9321 | 1.8926 | 0.5243 | 2.4999 | 0.0153 | -0.0224 | 0.2521 | 0.2692 | -0.0704 | 0.1936 | 0.0851 | -0.1455 | 0.0924 | 0.1972 | 0.0478 | -0.0389 | 0.0432 | -0.0616 | 0.0828 | -46.6908 | -5.137 | -18.9679 | 12 | 0.7276 | -0.2755 | -0.1273 | 0.3282 | -0.2467 | 0.408 | 0.0038 | -0.0775 | -0.0318 | 0.445 | -0.1565 | 0.0302 | 0.1977 | 0.0254 | 0.0894 | 0.1697 | -0.2229 | 0.0955 | -0.1486 | 0.0883 | 0.376 | -48.7489 | -13.8416 | -21.3997 | 13 | 2.0521 | -0.2031 | 0.5826 | 1.3103 | -0.246 | 2.0335 | -0.0646 | 0.0927 | -0.2563 | 0.1356 | 0.0265 | 0.1674 | 0.1822 | 0.1908 | 0.0264 | 0.2627 | -0.0033 | -0.0514 | 0.0617 | -0.0185 | 0.1761 | -45.7503 | -7.0032 | -18.6027 | 14 | 1.8374 | 0.7288 | 0.3549 | 2.608 | 0.5457 | 1.777 | 0.134 | -0.2135 | 0.2029 | 0.5346 | -0.2105 | 0.6639 | -0.1936 | -0.284 | -0.0063 | 0.2687 | -0.0122 | 0.0996 | 0.1131 | 0.0407 | 0.5124 | -52.3359 | -6.1982 | -11.056 | 15 | 3.5859 | -0.5327 | -1.7303 | 3.2013 | 0.5132 | 3.1206 | 0.102 | -0.5554 | 0.3041 | -0.3451 | 0.0901 | -0.6893 | -0.4804 | 0.9443 | 0.0224 | 0.511 | -0.2231 | 0.2071 | 0.6352 | 0.1251 | 0.3384 | -20.4373 | -8.2884 | -43.4597 | 16 | 0.815 | -0.4854 | 0.3335 | 1.0734 | -0.388 | 0.1813 | -0.862 | -0.3253 | -0.1479 | -0.0862 | 0.3249 | -0.9865 | 0.1989 | 1.705 | -0.2465 | 0.432 | 0.215 | 0.0819 | 1.5961 | -0.076 | 0.6334 | -9.863 | -12.5499 | -41.001 | 17 | 0.7465 | -0.0798 | 0.5669 | 1.8799 | 0.9276 | 0.9421 | -0.5128 | -0.5177 | -0.5468 | -0.3909 | 0.0652 | -0.616 | 1.0303 | 1.856 | 0.1361 | 0.6337 | 0.3598 | 0.2591 | 1.1321 | 0.1027 | 0.6255 | -14.3842 | -18.8824 | -43.5345 | 18 | 0.2546 | 0.7998 | -0.1878 | 2.8738 | 0.2603 | 2.2817 | -0.1404 | -0.5073 | -0.6476 | 0.2655 | 0.1737 | -0.5826 | 0.9716 | 1.2954 | -0.0947 | 0.5345 | 0.1789 | 0.0394 | 1.0189 | -0.0739 | 0.3271 | -21.4077 | -15.6104 | -39.905 |
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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 100 through 119 )H100 - 119 | 2 | X-RAY DIFFRACTION | 2 | chain 'H' and (resid 120 through 167 )H120 - 167 | 3 | X-RAY DIFFRACTION | 3 | chain 'H' and (resid 168 through 195 )H168 - 195 | 4 | X-RAY DIFFRACTION | 4 | chain 'H' and (resid 196 through 223 )H196 - 223 | 5 | X-RAY DIFFRACTION | 5 | chain 'L' and (resid 1 through 18 )L1 - 18 | 6 | X-RAY DIFFRACTION | 6 | chain 'L' and (resid 19 through 38 )L19 - 38 | 7 | X-RAY DIFFRACTION | 7 | chain 'L' and (resid 39 through 61 )L39 - 61 | 8 | X-RAY DIFFRACTION | 8 | chain 'L' and (resid 62 through 90 )L62 - 90 | 9 | X-RAY DIFFRACTION | 9 | chain 'L' and (resid 91 through 102 )L91 - 102 | 10 | X-RAY DIFFRACTION | 10 | chain 'L' and (resid 103 through 114 )L103 - 114 | 11 | X-RAY DIFFRACTION | 11 | chain 'L' and (resid 115 through 151 )L115 - 151 | 12 | X-RAY DIFFRACTION | 12 | chain 'L' and (resid 152 through 164 )L152 - 164 | 13 | X-RAY DIFFRACTION | 13 | chain 'L' and (resid 165 through 199 )L | | | | | | | | | | | | | | | | | | | | | | | | | |
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