ソフトウェア | 名称 | バージョン | 分類 |
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CrystalClear | | データ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.6.4_486)精密化 | MOSFLM | | データ削減 | SCALA | | 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: 単波長異常分散 / 解像度: 1.7→37.292 Å / SU ML: 0.24 / σ(F): 1.08 / 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 | 0.2194 | 6992 | 5.02 % | random |
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Rwork | 0.1935 | - | - | - |
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all | 0.1949 | 72978 | - | - |
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obs | 0.1949 | 139416 | 96.17 % | - |
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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: 33.038 Å2 / ksol: 0.359 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- | 5.3911 Å2 | -0 Å2 | -1.5094 Å2 |
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2- | - | 0.3718 Å2 | 0 Å2 |
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3- | - | - | -5.7629 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→37.292 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4958 | 0 | 14 | 316 | 5288 |
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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 | 5099 | X-RAY DIFFRACTION | f_angle_d0.995 | 6896 | X-RAY DIFFRACTION | f_dihedral_angle_d12.93 | 1957 | X-RAY DIFFRACTION | f_chiral_restr0.067 | 774 | X-RAY DIFFRACTION | f_plane_restr0.004 | 899 | | | | | |
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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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1.7004-1.7197 | 0.344 | 134 | 0.3017 | 2904 | X-RAY DIFFRACTION | 63 | 1.7197-1.7399 | 0.3545 | 158 | 0.2999 | 3419 | X-RAY DIFFRACTION | 74 | 1.7399-1.7611 | 0.2689 | 205 | 0.2723 | 3733 | X-RAY DIFFRACTION | 81 | 1.7611-1.7834 | 0.2861 | 207 | 0.2788 | 3939 | X-RAY DIFFRACTION | 86 | 1.7834-1.8069 | 0.3201 | 235 | 0.2648 | 4214 | X-RAY DIFFRACTION | 91 | 1.8069-1.8316 | 0.3034 | 221 | 0.2538 | 4311 | X-RAY DIFFRACTION | 95 | 1.8316-1.8578 | 0.2624 | 213 | 0.246 | 4532 | X-RAY DIFFRACTION | 98 | 1.8578-1.8855 | 0.2744 | 220 | 0.2247 | 4640 | X-RAY DIFFRACTION | 100 | 1.8855-1.915 | 0.2625 | 237 | 0.2169 | 4502 | X-RAY DIFFRACTION | 100 | 1.915-1.9464 | 0.2393 | 219 | 0.2044 | 4611 | X-RAY DIFFRACTION | 100 | 1.9464-1.98 | 0.2508 | 270 | 0.2062 | 4652 | X-RAY DIFFRACTION | 100 | 1.98-2.016 | 0.2407 | 210 | 0.2034 | 4559 | X-RAY DIFFRACTION | 100 | 2.016-2.0547 | 0.2078 | 228 | 0.1972 | 4658 | X-RAY DIFFRACTION | 100 | 2.0547-2.0967 | 0.2355 | 217 | 0.1934 | 4539 | X-RAY DIFFRACTION | 100 | 2.0967-2.1422 | 0.2434 | 257 | 0.1837 | 4574 | X-RAY DIFFRACTION | 100 | 2.1422-2.1921 | 0.2098 | 223 | 0.1825 | 4649 | X-RAY DIFFRACTION | 100 | 2.1921-2.2469 | 0.2311 | 249 | 0.1895 | 4563 | X-RAY DIFFRACTION | 100 | 2.2469-2.3076 | 0.2145 | 244 | 0.185 | 4565 | X-RAY DIFFRACTION | 100 | 2.3076-2.3755 | 0.2594 | 252 | 0.1788 | 4604 | X-RAY DIFFRACTION | 100 | 2.3755-2.4522 | 0.1782 | 252 | 0.1878 | 4560 | X-RAY DIFFRACTION | 100 | 2.4522-2.5398 | 0.2242 | 241 | 0.1868 | 4601 | X-RAY DIFFRACTION | 100 | 2.5398-2.6415 | 0.1961 | 288 | 0.1979 | 4540 | X-RAY DIFFRACTION | 100 | 2.6415-2.7617 | 0.2458 | 237 | 0.2023 | 4590 | X-RAY DIFFRACTION | 100 | 2.7617-2.9072 | 0.2148 | 242 | 0.2051 | 4584 | X-RAY DIFFRACTION | 100 | 2.9072-3.0893 | 0.2444 | 237 | 0.218 | 4595 | X-RAY DIFFRACTION | 100 | 3.0893-3.3277 | 0.2128 | 252 | 0.2115 | 4591 | X-RAY DIFFRACTION | 100 | 3.3277-3.6623 | 0.2279 | 277 | 0.2067 | 4532 | X-RAY DIFFRACTION | 100 | 3.6623-4.1916 | 0.1868 | 288 | 0.1608 | 4565 | X-RAY DIFFRACTION | 100 | 4.1916-5.2786 | 0.1723 | 234 | 0.1461 | 4581 | X-RAY DIFFRACTION | 100 | 5.2786-37.3009 | 0.1953 | 245 | 0.1717 | 4517 | X-RAY DIFFRACTION | 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 | 1.2858 | 0.1478 | 0.566 | 0.9089 | 0.1088 | 1.1103 | 0.1167 | -0.0802 | -0.2055 | -0.3698 | -0.0566 | -0.064 | 0.4216 | -0.047 | -0.1131 | 0.2906 | -0.0226 | -0.0393 | 0.1381 | -0.013 | 0.1835 | 25.9182 | -9.2459 | -58.8719 | 2 | 2.9907 | -0.9541 | -0.2951 | 2.3238 | 0.9169 | 0.5339 | 0.1464 | -0.1652 | 0.5494 | -0.6157 | 0.005 | 0.0811 | -0.2658 | -0.1398 | -0.073 | 0.2249 | 0.0321 | -0.0505 | 0.1437 | -0.0357 | 0.2335 | 23.6037 | -0.1138 | -57.5298 | 3 | 1.415 | -0.0203 | 0.4374 | 0.7644 | 0.3824 | 1.5672 | -0.0274 | -0.2259 | 0.1075 | -0.0261 | -0.0599 | 0.0739 | 0.009 | -0.3151 | 0.0728 | 0.0743 | -0.0112 | -0.0057 | 0.1549 | -0.0428 | 0.1654 | 30.6914 | 0.332 | -42.2988 | 4 | 0.565 | -0.229 | 0.2658 | 0.3486 | -0.4179 | 0.4771 | -0.0186 | -0.1043 | -0.0978 | 0.0516 | 0.0504 | 0.178 | 0.0212 | -0.2102 | 0.0078 | 0.0708 | -0.0097 | 0.0234 | 0.1436 | -0.0198 | 0.1674 | 39.7873 | -1.3159 | -37.0961 | 5 | 0.6184 | -0.0586 | -0.0944 | 1.8049 | -0.4247 | 0.8659 | -0.0034 | -0.0722 | 0.0843 | -0.157 | -0.0879 | -0.0862 | 0.0339 | 0.0035 | 0.011 | 0.0658 | -0.0156 | 0.0176 | 0.0853 | -0.0015 | 0.1265 | 51.7498 | 0.1062 | -43.3295 | 6 | 1.1143 | -0.4435 | -0.1219 | 0.5456 | -0.1931 | 1.1133 | -0.2253 | -0.1954 | 0.0063 | 0.1301 | 0.2111 | -0.0334 | 0.5796 | -0.1761 | 0.0173 | 0.247 | -0.044 | 0.0125 | 0.1878 | 0.0565 | 0.1465 | 48.7478 | -11.5104 | -29.4075 | 7 | 0.3109 | 0.746 | 0.4185 | 2.0341 | 1.0634 | 1.6307 | -0.1148 | -0.0565 | 0.0619 | -0.0236 | -0.1006 | 0.4008 | 0.2808 | -0.0784 | 0.1888 | 0.2 | -0.0179 | 0.0106 | 0.2023 | -0.0324 | 0.2296 | 53.5371 | -3.0148 | -113.249 | 8 | 4.7637 | 0.6342 | 0.1007 | 0.0899 | -0.0338 | 1.4764 | -0.573 | -0.35 | 0.9633 | 0.0527 | 0.1074 | 0.2322 | -0.2163 | 0.1373 | 0.3357 | 0.444 | 0.0234 | 0.0145 | 0.305 | -0.1481 | 0.3946 | 60.8464 | 8.3654 | -102.8286 | 9 | 2.565 | -0.0702 | -0.4074 | 0.4204 | 0.7795 | 2.7056 | -0.0961 | -0.413 | -0.3044 | 0.2372 | 0.056 | 0.2205 | 1.1696 | -0.1207 | 0.0748 | 0.3968 | 0.0092 | 0.0119 | 0.1727 | -0.0067 | 0.1783 | 60.223 | -8.4011 | -107.1992 | 10 | 0.667 | 0.0998 | -0.5814 | 0.5438 | -0.452 | 2.5943 | 0.007 | 0.3046 | -0.0393 | -0.1823 | -0.0367 | -0.0852 | 0.54 | 0.3379 | 0.0089 | 0.2681 | 0.1023 | -0.0148 | 0.283 | -0.0154 | 0.1374 | 66.2067 | -7.4851 | -93.6413 | 11 | 0.9112 | 1.0758 | -0.4407 | 1.5196 | 0.2597 | 2.3134 | 0.1148 | 0.1794 | 0.1601 | -0.1417 | -0.0743 | 0.2776 | 0.2056 | -0.1699 | -0.0171 | 0.1516 | 0.0364 | -0.0151 | 0.1884 | -0.012 | 0.163 | 57.1114 | -1.8785 | -82.3469 | 12 | 0.7432 | -0.6137 | -0.0859 | 0.8665 | -0.1872 | 2.5993 | 0.0073 | -0.0734 | 0.0028 | 0.2953 | 0.0253 | 0.1127 | 0.1826 | 0.016 | -0.0373 | 0.2102 | 0.0062 | 0.0161 | 0.1559 | -0.0032 | 0.1268 | 59.0621 | -2.3913 | -74.5709 |
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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 A and resid 2:51)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 52:73)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 74:140)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 141:175)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 176:277)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 278:308)7 | X-RAY DIFFRACTION | 7 | (chain B and resid -11:39) | 8 | X-RAY DIFFRACTION | 8 | (chain B and resid 40:52)9 | X-RAY DIFFRACTION | 9 | (chain B and resid 53:77)10 | X-RAY DIFFRACTION | 10 | (chain B and resid 78:140)11 | X-RAY DIFFRACTION | 11 | (chain B and resid 141:210)12 | X-RAY DIFFRACTION | 12 | (chain B and resid 211:306) | | | | | | | | | | |
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