ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALEPACK | | データスケーリング | | PHENIX | 1.7.3_928精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | HKL-2000 | | データ収集 | | HKL-2000 | | データ削減 | | HKL2Map | | 位相決定 | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.395→37.67 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.19 / σ(F): 1.36 / 位相誤差: 16.01 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1773 | 7698 | 10 % |
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Rwork | 0.1645 | - | - |
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obs | 0.1657 | 77006 | 99.47 % |
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all | - | 77074 | - |
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溶媒の処理 | 減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 42.142 Å2 / ksol: 0.347 e/Å3 |
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原子変位パラメータ | Biso max: 79 Å2 / Biso mean: 25.4023 Å2 / Biso min: 10.08 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.657 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 1.1565 Å2 | -0 Å2 |
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3- | - | - | -1.8135 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.395→37.67 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2541 | 0 | 26 | 479 | 3046 |
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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_d0.005 | 2698 | X-RAY DIFFRACTION | f_angle_d1.017 | 3668 | X-RAY DIFFRACTION | f_chiral_restr0.056 | 385 | X-RAY DIFFRACTION | f_plane_restr0.005 | 482 | X-RAY DIFFRACTION | f_dihedral_angle_d14.406 | 992 | | | | | |
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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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1.395-1.4113 | 0.3285 | 226 | 0.3158 | 2049 | 2275 | 89 | 1.4113-1.4279 | 0.3231 | 254 | 0.3024 | 2280 | 2534 | 100 | 1.4279-1.4453 | 0.2844 | 255 | 0.2745 | 2306 | 2561 | 100 | 1.4453-1.4636 | 0.2708 | 254 | 0.2464 | 2275 | 2529 | 100 | 1.4636-1.4828 | 0.2608 | 256 | 0.2297 | 2306 | 2562 | 100 | 1.4828-1.5031 | 0.2381 | 256 | 0.2167 | 2302 | 2558 | 100 | 1.5031-1.5246 | 0.2306 | 255 | 0.2082 | 2299 | 2554 | 100 | 1.5246-1.5474 | 0.2113 | 254 | 0.1911 | 2280 | 2534 | 100 | 1.5474-1.5715 | 0.2154 | 255 | 0.1822 | 2297 | 2552 | 100 | 1.5715-1.5973 | 0.2007 | 258 | 0.177 | 2323 | 2581 | 100 | 1.5973-1.6249 | 0.1907 | 253 | 0.1685 | 2268 | 2521 | 100 | 1.6249-1.6544 | 0.1827 | 255 | 0.1569 | 2298 | 2553 | 100 | 1.6544-1.6862 | 0.1924 | 258 | 0.1606 | 2323 | 2581 | 100 | 1.6862-1.7206 | 0.1761 | 257 | 0.1549 | 2310 | 2567 | 100 | 1.7206-1.7581 | 0.1791 | 253 | 0.1565 | 2279 | 2532 | 100 | 1.7581-1.799 | 0.1724 | 258 | 0.1595 | 2322 | 2580 | 100 | 1.799-1.8439 | 0.1738 | 255 | 0.1588 | 2294 | 2549 | 100 | 1.8439-1.8938 | 0.183 | 259 | 0.1607 | 2334 | 2593 | 100 | 1.8938-1.9495 | 0.1821 | 256 | 0.1569 | 2300 | 2556 | 100 | 1.9495-2.0124 | 0.1678 | 255 | 0.1561 | 2298 | 2553 | 100 | 2.0124-2.0844 | 0.1718 | 260 | 0.1591 | 2336 | 2596 | 100 | 2.0844-2.1678 | 0.1791 | 256 | 0.1556 | 2306 | 2562 | 100 | 2.1678-2.2665 | 0.153 | 260 | 0.1483 | 2344 | 2604 | 100 | 2.2665-2.3859 | 0.1575 | 259 | 0.1414 | 2333 | 2592 | 100 | 2.3859-2.5354 | 0.166 | 258 | 0.1479 | 2326 | 2584 | 100 | 2.5354-2.7311 | 0.1729 | 263 | 0.158 | 2361 | 2624 | 100 | 2.7311-3.0058 | 0.1872 | 262 | 0.1672 | 2354 | 2616 | 100 | 3.0058-3.4405 | 0.1714 | 263 | 0.1636 | 2375 | 2638 | 100 | 3.4405-4.3337 | 0.1474 | 264 | 0.1489 | 2385 | 2649 | 100 | 4.3337-37.67 | 0.1832 | 271 | 0.1754 | 2445 | 2716 | 97 |
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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 | 1.6674 | 0.1509 | -0.1313 | 1.0727 | -0.5776 | 0.8466 | 0.0587 | 0.0716 | -0.247 | -0.1294 | -0.224 | -0.0888 | 0.2549 | 0.1439 | -0.0083 | 0.2254 | 0.0333 | 0.0627 | 0.1735 | 0.0281 | 0.203 | 20.0066 | 33.4708 | -2.2247 | 2 | 0.6768 | 0.0001 | 0.0188 | 0.8885 | -0.1718 | 0.9605 | -0.0135 | -0.0203 | -0.0354 | 0.0181 | -0.1142 | -0.1448 | 0.1001 | 0.1446 | 0.0001 | 0.1672 | 0.0316 | 0.0398 | 0.162 | 0.0463 | 0.1789 | 18.9038 | 38.2577 | 3.2341 | 3 | 2.8859 | -0.2505 | 0.6041 | 1.7421 | -0.1584 | 0.8359 | -0.0137 | -0.1843 | -0.5889 | 0.3674 | 0.182 | 0.3854 | 0.2211 | -0.4641 | 0.0706 | 0.1943 | -0.0107 | 0.0671 | 0.2199 | 0.0672 | 0.2916 | 4.2106 | 31.8164 | 9.147 | 4 | 0.9246 | -0.2766 | -0.2052 | 1.6567 | -0.1767 | 0.9871 | -0.0673 | 0.0288 | -0.1513 | 0.0127 | 0.0406 | 0.117 | 0.1324 | -0.1437 | -0.0301 | 0.154 | -0.0123 | 0.0294 | 0.1426 | 0.0216 | 0.1631 | 6.8606 | 37.0407 | 2.8005 | 5 | 0.9981 | 0.0345 | -0.3807 | 0.5856 | -0.0504 | 0.8085 | 0.029 | -0.0273 | 0.2727 | 0.0608 | 0.1085 | 0.0329 | -0.0968 | -0.0944 | 0.008 | 0.1504 | 0.0338 | 0.0391 | 0.1601 | 0.0308 | 0.1888 | 5.6656 | 51.7453 | 4.0227 | 6 | 4.911 | -0.5823 | -1.0686 | 1.5118 | -1.6046 | 2.3699 | -0.1761 | -0.5884 | 0.3488 | 0.2687 | 0.0473 | -0.2572 | -0.2397 | 0.6127 | 0.0213 | 0.2389 | 0.0022 | -0.0127 | 0.404 | -0.0887 | 0.2043 | 14.052 | 52.4388 | 14.3613 | 7 | 0.5098 | -0.1959 | -0.408 | 1.1209 | -0.2628 | 2.2228 | 0.2512 | 0.1071 | 0.4822 | 0.129 | -0.0979 | -0.031 | -0.3754 | 0.3511 | 0.1659 | 0.1968 | -0.0014 | 0.0684 | 0.1978 | 0.0434 | 0.2782 | 11.8358 | 58.0197 | -0.3995 | 8 | 1.9041 | -0.6974 | -0.6047 | 2.1797 | -0.3504 | 1.9418 | -0.1068 | -0.1416 | 0.046 | -0.1286 | 0.1835 | 0.2557 | -0.2057 | -0.3019 | 0.043 | 0.1402 | 0.002 | 0.0342 | 0.2441 | 0.0291 | 0.1825 | -23.0251 | 47.7542 | 22.8269 | 9 | 1.0163 | -0.1283 | 0.2538 | 1.3803 | 0.1945 | 0.6079 | -0.0665 | -0.4068 | 0.0783 | 0.1074 | 0.0568 | 0.0189 | -0.144 | -0.1637 | 0.0054 | 0.2123 | 0.047 | 0.0354 | 0.1718 | -0.0171 | 0.1434 | -15.277 | 48.7494 | 27.6349 | 10 | 1.0798 | -0.4029 | 0.6615 | 1.0348 | -0.5991 | 1.8589 | -0.0385 | 0.1122 | 0.0174 | 0.0091 | 0.0183 | -0.0479 | 0.1 | 0.1545 | 0.0022 | 0.13 | 0.021 | 0.005 | 0.1346 | 0.0025 | 0.1252 | -7.3558 | 43.2218 | 17.7573 | 11 | 1.3072 | -0.6905 | 0.3818 | 1.796 | -0.6463 | 1.104 | -0.0708 | -0.0883 | 0.1696 | 0.4305 | -0.0016 | -0.2874 | -0.0808 | 0.0992 | 0.0104 | 0.1738 | 0.0448 | -0.0558 | 0.1729 | -0.0363 | 0.1785 | 2.8129 | 42.407 | 30.7698 |
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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 (resseq 48:81)A48 - 81 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 82:118)A82 - 118 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 119:134)A119 - 134 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 135:163)A135 - 163 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 164:191)A164 - 191 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 192:200)A192 - 200 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 201:220)A201 - 220 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq 61:81)B61 - 81 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 82:106)B82 - 106 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 107:191)B107 - 191 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 192:220)B192 - 220 | | | | | | | | | | | | | | | | | | | | | | |
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