ソフトウェア | 名称 | バージョン | 分類 |
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Blu-Ice | | データ収集 | MOSFLM | 7.0.9データ削減 | Aimless | 0.2.7データスケーリング | PHENIX | 1.9-1692 | 位相決定 | PHENIX | 1.9-1692 | 精密化 | Coot | 0.7.2モデル構築 | PDB_EXTRACT | 3.15 | データ抽出 | | | |
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精密化 | 構造決定の手法: 単一同系置換・異常分散 / 解像度: 2.124→43.84 Å / SU ML: 0.24 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 24.68 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2294 | 1031 | 2.57 % | Random selection |
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Rwork | 0.2031 | 39108 | - | - |
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obs | 0.2038 | 40139 | 99.98 % | - |
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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: 141.29 Å2 / Biso mean: 56.7806 Å2 / Biso min: 25.16 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.124→43.84 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4739 | 0 | 11 | 195 | 4945 |
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Biso mean | - | - | 77.07 | 51.15 | - |
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残基数 | - | - | - | - | 582 |
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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 | 4838 | X-RAY DIFFRACTION | f_angle_d0.712 | 6534 | X-RAY DIFFRACTION | f_chiral_restr0.026 | 738 | X-RAY DIFFRACTION | f_plane_restr0.004 | 825 | X-RAY DIFFRACTION | f_dihedral_angle_d14.247 | 1809 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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2.1241-2.2361 | 0.3465 | 143 | 0.2858 | 5485 | 5628 | 2.2361-2.3762 | 0.276 | 152 | 0.2527 | 5506 | 5658 | 2.3762-2.5596 | 0.2519 | 153 | 0.2333 | 5516 | 5669 | 2.5596-2.8171 | 0.301 | 132 | 0.2328 | 5564 | 5696 | 2.8171-3.2247 | 0.2783 | 127 | 0.2183 | 5586 | 5713 | 3.2247-4.0623 | 0.2178 | 158 | 0.1847 | 5614 | 5772 | 4.0623-43.8491 | 0.1853 | 166 | 0.177 | 5837 | 6003 |
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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 | 2.2669 | 1.8453 | -0.5665 | 6.0565 | -1.9167 | 2.6134 | 0.0617 | -0.2314 | 0.1783 | 0.3134 | 0.0446 | 0.3662 | 0.068 | -0.6961 | -0.1205 | 0.283 | -0.0273 | 0.0071 | 0.5381 | -0.0232 | 0.3088 | -7.2431 | 60.5744 | 108.8994 | 2 | 4.6191 | 4.5459 | -3.9389 | 7.9746 | -5.3798 | 4.9392 | 0.3328 | -0.3074 | 0.4592 | 0.6834 | -0.2086 | 0.0964 | -0.4689 | 0.0059 | -0.1849 | 0.3771 | 0.0834 | -0.044 | 0.2643 | -0.0872 | 0.4343 | 6.7155 | 82.2627 | 103.8029 | 3 | 4.4596 | 0.2952 | -0.9667 | 7.6821 | -0.0499 | 3.3773 | 0.0236 | -0.4987 | -0.726 | 0.9522 | -0.0871 | 0.1137 | 0.9262 | -0.8304 | 0.1874 | 0.432 | -0.1687 | -0.0835 | 0.505 | 0.1392 | 0.3932 | -7.079 | 43.3545 | 113.8734 | 4 | 3.4726 | 3.3369 | 4.5544 | 4.2872 | 4.3972 | 5.9827 | 0.0426 | -0.0331 | 1.5501 | -0.1508 | -0.1855 | 0.03 | 0.2103 | -0.0783 | 0.1238 | 0.6122 | -0.0037 | 0.1102 | 0.5943 | -0.1387 | 0.8546 | 11.112 | 51.3327 | 96.2481 | 5 | 4.6997 | 0.2521 | -1.3407 | 5.6591 | -1.6652 | 3.9498 | -0.1219 | -0.1629 | 0.4843 | -0.0581 | 0.2022 | 0.0486 | -0.3606 | 0.0644 | -0.0592 | 0.2336 | 0.0083 | -0.033 | 0.2514 | -0.054 | 0.4401 | 24.0515 | 76.1687 | 96.8789 | 6 | 5.0795 | 3.6897 | -1.4321 | 5.5318 | -2.4752 | 3.4826 | 0.2835 | -0.3841 | -0.7104 | 0.294 | -0.3356 | -0.8071 | 0.4625 | -0.0847 | 0.1194 | 0.3212 | -0.0409 | -0.0928 | 0.2694 | 0.0294 | 0.4128 | 5.0689 | 50.2891 | 108.5028 | 7 | 4.201 | 1.9938 | -4.8754 | 6.2943 | -4.2619 | 8.091 | -0.1385 | 0.4118 | 0.0734 | -0.4864 | -0.0942 | -0.0635 | -0.3278 | -0.187 | 0.1265 | 0.3372 | 0.1011 | -0.0383 | 0.3117 | 0.0018 | 0.5326 | 17.8514 | 76.4071 | 89.2208 | 8 | 6.0012 | 1.7943 | 1.075 | 7.9504 | 0.9845 | 6.9698 | -0.3828 | 0.1157 | 0.3064 | 0.0213 | -0.0222 | -0.0374 | 0.3366 | -0.8685 | 0.3366 | 0.3309 | -0.0159 | 0.0992 | 0.4699 | -0.1216 | 0.4525 | 27.2384 | 47.8528 | 75.8938 | 9 | 6.6896 | 0.4457 | -6.1026 | 5.0246 | -3.3321 | 8.0388 | -0.7073 | -0.2403 | 0.401 | -0.7557 | 1.1195 | -0.4801 | -0.0627 | 1.5158 | -0.6462 | 1.1603 | -0.3076 | 0.1507 | 1.0662 | -0.2027 | 0.6432 | 13.8294 | 29.2802 | 69.568 | 10 | 3.2484 | 1.5321 | 2.3536 | 5.7702 | 5.1655 | 7.7698 | 0.1828 | 0.1631 | -0.1816 | 0.5821 | -0.0248 | -0.0302 | 1.0984 | -0.0135 | -0.2209 | 0.3865 | 0.0015 | 0.0248 | 0.2364 | 0.0784 | 0.3727 | 39.1267 | 47.6655 | 81.067 | 11 | 8.244 | 5.1066 | 5.7163 | 4.7411 | 5.7935 | 7.5795 | -0.4405 | 0.72 | 0.0972 | -0.3545 | 0.4103 | -0.05 | -0.2759 | 0.6311 | 0.1532 | 0.3899 | -0.0273 | -0.0424 | 0.2915 | 0.1249 | 0.3597 | 40.2895 | 55.7239 | 75.3217 | 12 | 1.2213 | 0.7717 | 0.7343 | 1.8703 | 0.0671 | 1.3527 | -0.141 | 0.4963 | 0.0824 | 0.12 | -0.2881 | 0.8284 | 1.1822 | -1.0151 | 0.2096 | 0.6931 | -0.4759 | 0.1005 | 1.2258 | -0.1691 | 0.7403 | 8.1308 | 41.1748 | 72.1973 | 13 | 6.9079 | 0.3517 | 1.4388 | 4.0704 | 0.7486 | 3.9993 | -0.0327 | 0.0244 | 0.3927 | -0.2858 | -0.0024 | -0.4434 | -0.3638 | 0.33 | 0.0178 | 0.3222 | -0.0127 | 0.0785 | 0.2295 | 0.0259 | 0.4587 | 34.0364 | 73.6256 | 88.3905 | 14 | 2.6557 | 2.6624 | 0.886 | 5.0397 | 2.1241 | 3.598 | -0.2265 | 0.297 | -0.1762 | -0.3446 | 0.119 | 0.1729 | 0.3164 | -0.6483 | 0.1322 | 0.2972 | -0.0714 | 0.0306 | 0.435 | -0.0198 | 0.5386 | 20.0339 | 55.0262 | 80.1699 |
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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 158:235)A158 - 235 | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 236:279)A236 - 279 | 3 | X-RAY DIFFRACTION | 3 | (chain A and resid 280:320)A280 - 320 | 4 | X-RAY DIFFRACTION | 4 | (chain A and resid 321:327)A321 - 327 | 5 | X-RAY DIFFRACTION | 5 | (chain A and resid 328:363)A328 - 363 | 6 | X-RAY DIFFRACTION | 6 | (chain A and resid 364:426)A364 - 426 | 7 | X-RAY DIFFRACTION | 7 | (chain A and resid 427:456)A427 - 456 | 8 | X-RAY DIFFRACTION | 8 | (chain B and resid 160:193)B160 - 193 | 9 | X-RAY DIFFRACTION | 9 | (chain B and resid 194:206)B194 - 206 | 10 | X-RAY DIFFRACTION | 10 | (chain B and resid 207:247)B207 - 247 | 11 | X-RAY DIFFRACTION | 11 | (chain B and resid 248:288)B248 - 288 | 12 | X-RAY DIFFRACTION | 12 | (chain B and resid 289:326)B289 - 326 | 13 | X-RAY DIFFRACTION | 13 | (chain B and resid 327:370)B327 - 370 | 14 | X-RAY DIFFRACTION | 14 | (chain B and resid 371:451)B371 - 451 | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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