ソフトウェア | 名称 | バージョン | 分類 |
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Aimless | 0.1.27データスケーリング | RESOLVE | 2.13 | 位相決定 | PHENIX | | 精密化 | PDB_EXTRACT | 3.2 | データ抽出 | XSCALE | | データスケーリング | SHELXD | | 位相決定 | XDS | | データ削減 | |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 2.4→29.658 Å / SU ML: 0.27 / 交差検証法: FREE R-VALUE / σ(F): 1.92 / 位相誤差: 20.79
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2026 | 9569 | 5.02 % |
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Rwork | 0.1765 | - | - |
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obs | 0.1778 | 190646 | 98.99 % |
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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 |
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原子変位パラメータ | Biso max: 240.53 Å2 / Biso mean: 62.5588 Å2 / Biso min: 25.48 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.4→29.658 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 26350 | 0 | 160 | 753 | 27263 |
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Biso mean | - | - | 87.18 | 53.85 | - |
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残基数 | - | - | - | - | 3210 |
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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_d0.006 | 27098 | X-RAY DIFFRACTION | f_angle_d0.915 | 36570 | X-RAY DIFFRACTION | f_chiral_restr0.034 | 3980 | X-RAY DIFFRACTION | f_plane_restr0.005 | 4630 | X-RAY DIFFRACTION | f_dihedral_angle_d12.462 | 9970 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | Rms | タイプ |
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1 | 1 | A19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 2 | B19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 3 | C19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 4 | D19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 5 | E19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 6 | F19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 7 | G19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 8 | H19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 9 | I19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL1 | 10 | J19833 | X-RAY DIFFRACTION | 9.032 | TORSIONAL | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.3999-2.4272 | 0.301 | 333 | 0.2816 | 5885 | 6218 | 98 | 2.4272-2.4557 | 0.3127 | 322 | 0.2656 | 6066 | 6388 | 99 | 2.4557-2.4857 | 0.2821 | 280 | 0.259 | 5998 | 6278 | 99 | 2.4857-2.5171 | 0.2839 | 330 | 0.2544 | 6014 | 6344 | 99 | 2.5171-2.5502 | 0.2926 | 309 | 0.2532 | 6069 | 6378 | 99 | 2.5502-2.5851 | 0.2949 | 323 | 0.2504 | 5949 | 6272 | 99 | 2.5851-2.6221 | 0.2518 | 341 | 0.2405 | 6027 | 6368 | 99 | 2.6221-2.6612 | 0.2687 | 317 | 0.2362 | 6041 | 6358 | 99 | 2.6612-2.7027 | 0.2763 | 316 | 0.2337 | 6008 | 6324 | 99 | 2.7027-2.747 | 0.2437 | 339 | 0.2248 | 5991 | 6330 | 99 | 2.747-2.7943 | 0.2787 | 344 | 0.2268 | 6008 | 6352 | 99 | 2.7943-2.8451 | 0.2315 | 325 | 0.2185 | 6059 | 6384 | 99 | 2.8451-2.8998 | 0.2563 | 292 | 0.2137 | 6066 | 6358 | 99 | 2.8998-2.9589 | 0.2355 | 296 | 0.2132 | 5913 | 6209 | 98 | 2.9589-3.0232 | 0.2431 | 303 | 0.2186 | 6071 | 6374 | 99 | 3.0232-3.0935 | 0.2305 | 302 | 0.2124 | 6058 | 6360 | 99 | 3.0935-3.1707 | 0.2253 | 317 | 0.204 | 6058 | 6375 | 99 | 3.1707-3.2564 | 0.2518 | 342 | 0.2089 | 5997 | 6339 | 99 | 3.2564-3.3521 | 0.2231 | 318 | 0.1948 | 6061 | 6379 | 99 | 3.3521-3.4601 | 0.2101 | 374 | 0.1892 | 5996 | 6370 | 99 | 3.4601-3.5836 | 0.2182 | 323 | 0.1835 | 6041 | 6364 | 99 | 3.5836-3.7268 | 0.2049 | 323 | 0.1798 | 6048 | 6371 | 99 | 3.7268-3.896 | 0.1879 | 279 | 0.1676 | 6051 | 6330 | 98 | 3.896-4.101 | 0.1685 | 296 | 0.1465 | 6079 | 6375 | 99 | 4.101-4.3571 | 0.1634 | 330 | 0.1359 | 6066 | 6396 | 99 | 4.3571-4.6924 | 0.1503 | 320 | 0.1218 | 6092 | 6412 | 99 | 4.6924-5.1623 | 0.1384 | 343 | 0.1189 | 6036 | 6379 | 99 | 5.1623-5.9042 | 0.1749 | 299 | 0.1439 | 6053 | 6352 | 98 | 5.9042-7.4194 | 0.1926 | 321 | 0.1618 | 6125 | 6446 | 99 | 7.4194-29.6605 | 0.1503 | 312 | 0.1432 | 6151 | 6463 | 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 | 1.2569 | -0.0907 | -0.2617 | 2.2088 | 0.1341 | 1.0779 | 0.0071 | -0.2697 | -0.06 | 0.1989 | -0.0605 | -0.1581 | 0.1239 | 0.1199 | 0.0349 | 0.3569 | 0.0042 | 0.0361 | 0.6412 | 0.0725 | 0.2479 | -22.5789 | 72.7366 | 90.57 | 2 | 1.5985 | 0.1815 | -0.4821 | 2.0744 | -0.8451 | 1.8267 | 0.0853 | -0.382 | 0.1291 | 0.3256 | 0.0304 | 0.008 | -0.3011 | 0.1274 | -0.0817 | 0.4356 | -0.0599 | 0.0676 | 0.6229 | -0.0977 | 0.2818 | -23.6289 | 115.0459 | 88.5738 | 3 | 1.3507 | -0.387 | -1.026 | 1.5461 | 0.3963 | 2.7262 | 0.0812 | -0.2939 | 0.1888 | 0.098 | 0.0927 | -0.1424 | -0.368 | 0.4611 | -0.1126 | 0.3976 | -0.1208 | 0.0706 | 0.4461 | -0.0605 | 0.3008 | 0.0617 | 127.131 | 55.5698 | 4 | 0.8237 | 0.2847 | -0.2524 | 2.3447 | -0.2478 | 1.6234 | 0.0235 | -0.1868 | -0.0406 | 0.2992 | -0.0557 | -0.0788 | -0.0197 | 0.4024 | 0.0518 | 0.2088 | 0.0111 | -0.0045 | 0.5708 | 0.0069 | 0.2566 | 15.9116 | 92.4745 | 37.1095 | 5 | 1.8191 | -0.0528 | -0.2659 | 1.5629 | -0.2605 | 1.453 | -0.0633 | 0.129 | -0.146 | -0.1818 | -0.011 | 0.1144 | 0.2313 | -0.1309 | 0.0479 | 0.4673 | -0.0753 | 0.0456 | 0.4602 | -0.0975 | 0.332 | -44.0539 | 55.177 | 25.5123 | 6 | 1.9507 | 0.3708 | -0.8314 | 1.1884 | 0.0559 | 2.0683 | -0.0428 | -0.2411 | -0.1541 | 0.1577 | -0.0274 | -0.0989 | 0.1596 | 0.2525 | 0.0335 | 0.3801 | 0.1194 | 0.0484 | 0.4408 | 0.0764 | 0.3221 | 2.287 | 58.6915 | 58.9308 | 7 | 1.5063 | -0.2352 | -0.5575 | 2.5588 | -0.0034 | 1.2984 | -0.0902 | 0.2938 | 0.0037 | -0.0161 | -0.0015 | 0.22 | 0.115 | -0.2836 | 0.0723 | 0.3394 | -0.0546 | -0.0683 | 0.5766 | -0.0119 | 0.166 | -30.3031 | 88.7239 | 3.4494 | 8 | 1.589 | 0.0032 | -0.7506 | 1.2998 | 0.3592 | 2.0522 | 0.0703 | 0.2897 | 0.3238 | -0.1215 | 0.034 | 0.1746 | -0.3017 | -0.3698 | -0.0512 | 0.4376 | 0.1199 | -0.0496 | 0.459 | 0.0868 | 0.4274 | -46.0479 | 123.6142 | 21.5525 | 9 | 0.8178 | 0.4907 | -0.2311 | 2.5848 | -0.4885 | 1.3098 | 0.0613 | -0.0033 | 0.1404 | 0.0633 | -0.0054 | 0.3752 | -0.1777 | -0.27 | -0.0374 | 0.3075 | 0.1377 | 0.0288 | 0.5946 | -0.0388 | 0.4255 | -69.776 | 111.8436 | 54.803 | 10 | 1.099 | -0.3523 | -0.1271 | 1.334 | 0.2794 | 1.6133 | -0.1094 | 0.0155 | -0.0761 | 0.0083 | 0.1043 | 0.0601 | 0.168 | -0.2991 | 0.0127 | 0.3187 | -0.1161 | 0.0428 | 0.6289 | -0.002 | 0.2908 | -68.4751 | 69.4409 | 56.9854 |
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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 5 through 325 )A5 - 325 | 2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 5 through 325 )B5 - 325 | 3 | X-RAY DIFFRACTION | 3 | chain 'C' and (resid 5 through 325 )C5 - 325 | 4 | X-RAY DIFFRACTION | 4 | chain 'D' and (resid 5 through 325 )D5 - 325 | 5 | X-RAY DIFFRACTION | 5 | chain 'E' and (resid 5 through 325 )E5 - 325 | 6 | X-RAY DIFFRACTION | 6 | chain 'F' and (resid 5 through 325 )F5 - 325 | 7 | X-RAY DIFFRACTION | 7 | chain 'G' and (resid 5 through 325 )G5 - 325 | 8 | X-RAY DIFFRACTION | 8 | chain 'H' and (resid 5 through 325 )H5 - 325 | 9 | X-RAY DIFFRACTION | 9 | chain 'I' and (resid 5 through 325 )I5 - 325 | 10 | X-RAY DIFFRACTION | 10 | chain 'J' and (resid 5 through 325 )J5 - 325 | | | | | | | | | | | | | | | | | | | | |
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