ソフトウェア | 名称 | バージョン | 分類 |
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ADSC | Quantumデータ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.7_650)精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHENIX | | 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: PDB ENTRY 4IUP 解像度: 2.809→40.067 Å / SU ML: 0.45 / σ(F): 0.97 / 位相誤差: 25.15 / 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 | 0.2611 | 420 | 4.87 % | RANDOM |
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Rwork | 0.2008 | - | - | - |
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obs | 0.2038 | 16030 | 98.74 % | - |
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all | - | 16810 | - | - |
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溶媒の処理 | 減衰半径: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 12.237 Å2 / ksol: 0.304 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 6.1694 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.7714 Å2 | 0 Å2 |
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3- | - | - | -5.398 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.809→40.067 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2152 | 0 | 68 | 0 | 2220 |
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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_d0.019 | 2262 | X-RAY DIFFRACTION | f_angle_d1.692 | 3055 | X-RAY DIFFRACTION | f_dihedral_angle_d17.566 | 876 | X-RAY DIFFRACTION | f_chiral_restr0.102 | 339 | X-RAY DIFFRACTION | f_plane_restr0.006 | 392 | | | | | |
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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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2.8093-2.9853 | 0.3592 | 132 | 0.2933 | 2393 | X-RAY DIFFRACTION | 94 | 2.9853-3.2157 | 0.3327 | 148 | 0.2348 | 2562 | X-RAY DIFFRACTION | 100 | 3.2157-3.5391 | 0.22 | 135 | 0.2152 | 2555 | X-RAY DIFFRACTION | 100 | 3.5391-4.0508 | 0.2659 | 111 | 0.1873 | 2600 | X-RAY DIFFRACTION | 100 | 4.0508-5.1019 | 0.2461 | 126 | 0.1569 | 2570 | X-RAY DIFFRACTION | 100 | 5.1019-40.0714 | 0.234 | 128 | 0.2059 | 2570 | X-RAY DIFFRACTION | 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 | 0.3091 | 0.0381 | -0.0045 | 0.609 | -0.0147 | 0.0083 | -0.1281 | 0.1939 | 0.0573 | -0.0241 | 0.1401 | 0.072 | -0.0258 | 0.0881 | -0.1983 | 0.2351 | -0.1263 | 0.0222 | 0.3267 | 0.1247 | 0.1296 | 12.3524 | 26.3378 | 4.5629 | 2 | 0.6109 | -0.1463 | 0.7292 | 0.0987 | -0.3469 | 1.3341 | -0.1143 | -0.143 | 0.0583 | 0.1298 | 0.0381 | 0.1656 | -0.0799 | -0.2914 | -0.1338 | 0.1316 | -0.0311 | 0.0618 | 0.1897 | -0.0331 | 0.3213 | 4.4947 | 20.1306 | 8.7257 | 3 | 0.4733 | -0.0823 | -0.365 | 0.0511 | 0.0044 | 0.3353 | -0.3593 | -0.1393 | -0.0411 | 0.2814 | -0.1796 | -0.0532 | 0.1629 | 0.2802 | 0.0083 | 0.2792 | 0.0347 | -0.008 | 0.2366 | -0.0235 | 0.2176 | 12.9833 | 21.4208 | 23.6851 | 4 | 0.3 | 0.0665 | 0.2051 | 0.1218 | 0.0184 | 0.1595 | -0.0011 | -0.0239 | 0.0068 | 0.121 | -0.2757 | 0.1595 | 0.0359 | -0.3478 | 0.0349 | 0.0167 | -0.0141 | -0.0351 | 0.5202 | -0.086 | 0.2071 | 4.9063 | 25.708 | 14.1108 | 5 | 0.252 | 0.2375 | -0.0422 | 1.3722 | -0.17 | 0.9215 | 0.117 | 0.1053 | 0.2381 | 0.2368 | -0.2466 | -0.2886 | 0.0705 | 0.1121 | 0.0342 | 0.1673 | -0.0343 | 0.0516 | 0.2911 | -0.0062 | 0.2538 | 10.6915 | 20.605 | 12.5467 | 6 | 0.5972 | -0.2577 | -0.8404 | 0.1322 | 0.1424 | 3.1187 | 0.1093 | 0.0476 | -0.0314 | -0.2634 | -0.1725 | 0.0829 | -0.2499 | -0.0668 | -0.1267 | 0.2136 | 0.019 | -0.0205 | 0.079 | 0.081 | 0.3177 | 10.8796 | 23.3377 | -6.4245 | 7 | 0.6468 | 0.4853 | -0.1008 | 0.4069 | -0.2767 | 1.1163 | -0.2254 | 0.2027 | -0.3015 | -0.0185 | 0.2375 | -0.2019 | 0.4264 | 0.3387 | 0.1356 | 0.3433 | 0.1103 | -0.011 | 0.2526 | -0.0097 | 0.2741 | 15.9065 | 15.5167 | -12.6615 | 8 | 0.0029 | -0.0209 | -0.0389 | 0.2446 | 0.382 | 0.5978 | -0.2209 | -0.0666 | -0.0668 | 0.3921 | -0.3705 | 0.6943 | 0.0968 | -0.4982 | -0.5616 | 0.0396 | -0.2922 | -0.0114 | -0.165 | -0.1951 | 0.5567 | -0.1144 | 12.4557 | -2.0338 | 9 | 0.4279 | 0.2117 | -0.3069 | 0.8786 | -0.2769 | 1.3911 | -0.1599 | 0.2063 | -0.3954 | -0.2665 | -0.0768 | 0.0262 | 0.6528 | 0.0537 | 0.0279 | 0.3887 | 0.0429 | -0.0131 | 0.1788 | 0.0069 | 0.293 | 8.2384 | 11.5448 | -11.9841 | 10 | 0.3951 | 0.2947 | -0.1714 | 0.216 | -0.1275 | 0.0754 | 0.0809 | 0.0815 | -0.4587 | -0.1519 | 0.1541 | 0.0246 | 0.0612 | -0.0011 | -0.0801 | 0.6261 | -0.3959 | 0.078 | -0.0898 | -0.0179 | 0.3588 | 5.2757 | 5.3369 | -2.7775 | 11 | 0.1161 | -0.2201 | 0.2891 | 0.9141 | -0.009 | 1.3209 | 0.1134 | -0.0849 | 0.0174 | -0.0955 | 0.1424 | 0.0204 | -0.0274 | 0.1639 | 0.0873 | 0.101 | 0.0468 | 0.0408 | 0.3269 | -0.0066 | 0.1962 | 10.9903 | 18.1613 | -6.6562 | 12 | 0.2418 | -0.173 | 0.2145 | 0.6779 | 0.1037 | 0.4667 | 0.0486 | -0.0713 | -0.1663 | -0.0666 | 0.162 | 0.0818 | -0.1436 | -0.0407 | -0.0193 | 0.2 | 0.0204 | -0.0218 | 0.1511 | 0.0012 | 0.1894 | -11.1399 | 19.3613 | 36.8662 | 13 | 0.3874 | 0.3211 | -0.0807 | 0.6285 | 0.2298 | 0.7304 | 0.1363 | 0.0919 | -0.0647 | 0.529 | 0.1735 | -0.0644 | 0.5753 | -0.0874 | -0.0087 | 0.2617 | -0.0362 | -0.0705 | 0.2025 | 0.0112 | 0.1797 | -16.7398 | 16.3387 | 42.3093 | 14 | 0.5643 | -0.0862 | 0.0231 | 0.4525 | 0.5725 | 1.3836 | -0.1322 | 0.2694 | 0.2441 | -0.0504 | -0.0849 | 0.1922 | -0.4042 | 0.0278 | -0.0226 | 0.1621 | 0.0221 | -0.0131 | 0.2218 | 0.0099 | 0.1618 | -12.6242 | 17.4499 | 23.0494 | 15 | 0.2683 | 0.1267 | 0.0577 | 0.4656 | -0.2597 | 0.5886 | -0.2033 | -0.0324 | -0.1678 | 0.2128 | 0.1213 | -0.256 | 0.8568 | 0.3316 | 0.1001 | 0.5558 | 0.0524 | -0.0015 | 0.1801 | -0.0454 | 0.2617 | -14.6942 | 2.9854 | 25.657 | 16 | 0.9641 | -0.0623 | -0.2277 | 0.2257 | -0.0259 | 0.1381 | 0.0902 | 0.1694 | -0.0637 | -0.4197 | -0.0831 | -0.0016 | 0.4916 | -0.1308 | 0.0664 | 0.3962 | 0.0201 | -0.0665 | 0.2746 | -0.0248 | 0.2619 | -15.8171 | 7.6658 | 12.4101 | 17 | 1.2743 | 0.2836 | -0.0758 | 0.7363 | -0.8257 | 1.3105 | -0.1928 | -0.1379 | -0.3218 | -0.1387 | -0.3119 | -0.4592 | 0.2031 | 0.1547 | -0.0911 | 0.3242 | 0.0559 | 0.0024 | 0.1657 | -0.0955 | 0.2945 | -7.8935 | 3.1828 | 19.2829 | 18 | 0.3859 | -0.2915 | 0.0639 | 0.4328 | -0.0022 | 0.455 | 0.0862 | 0.5371 | 0.1503 | -0.0702 | 0.0479 | 0.026 | -0.0833 | -0.4706 | -0.0073 | 0.2632 | -0.0243 | -0.0083 | 0.3524 | -0.038 | 0.2915 | -15.5545 | 14.1328 | 18.4283 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'B' and (resseq 125:132)2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resseq 133:145)3 | X-RAY DIFFRACTION | 3 | chain 'B' and (resseq 146:155)4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resseq 156:169)5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resseq 170:181)6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resseq 182:187)7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resseq 188:198)8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq 199:209)9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 210:238)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 239:248)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 249:257)12 | X-RAY DIFFRACTION | 12 | chain 'A' and (resseq 124:155)13 | X-RAY DIFFRACTION | 13 | chain 'A' and (resseq 156:170)14 | X-RAY DIFFRACTION | 14 | chain 'A' and (resseq 171:198)15 | X-RAY DIFFRACTION | 15 | chain 'A' and (resseq 199:209)16 | X-RAY DIFFRACTION | 16 | chain 'A' and (resseq 210:232)17 | X-RAY DIFFRACTION | 17 | chain 'A' and (resseq 233:248)18 | X-RAY DIFFRACTION | 18 | chain 'A' and ( | | | | | | | | | | | | | | | | | |
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