ソフトウェア | 名称 | バージョン | 分類 |
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HKL-3000 | | データ削減 | PHENIX | | 精密化 | PDB_EXTRACT | 3.15 | データ抽出 | HKL-3000 | | 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: フーリエ合成 開始モデル: 4XGV 解像度: 1.747→33.922 Å / SU ML: 0.18 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 21.87 / 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 | 0.1985 | 5873 | 5.04 % | random selection |
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Rwork | 0.1718 | 110687 | - | - |
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obs | 0.1732 | 116560 | 96.55 % | - |
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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: 177.48 Å2 / Biso mean: 34.1684 Å2 / Biso min: 11.79 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.747→33.922 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 9432 | 0 | 47 | 679 | 10158 |
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Biso mean | - | - | 50.34 | 31.13 | - |
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残基数 | - | - | - | - | 1222 |
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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 | 9671 | X-RAY DIFFRACTION | f_angle_d0.874 | 13101 | X-RAY DIFFRACTION | f_chiral_restr0.033 | 1487 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1676 | X-RAY DIFFRACTION | f_dihedral_angle_d12.653 | 3579 | | | | | |
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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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1.7466-1.7664 | 0.2998 | 188 | 0.244 | 3192 | 3380 | 84 | 1.7664-1.7872 | 0.2712 | 176 | 0.2519 | 3667 | 3843 | 95 | 1.7872-1.809 | 0.285 | 168 | 0.2512 | 3637 | 3805 | 95 | 1.809-1.8319 | 0.3016 | 169 | 0.2579 | 3672 | 3841 | 95 | 1.8319-1.856 | 0.2732 | 199 | 0.2385 | 3645 | 3844 | 95 | 1.856-1.8814 | 0.2921 | 162 | 0.2356 | 3643 | 3805 | 96 | 1.8814-1.9083 | 0.2465 | 181 | 0.2184 | 3689 | 3870 | 95 | 1.9083-1.9368 | 0.227 | 215 | 0.2047 | 3593 | 3808 | 96 | 1.9368-1.967 | 0.2297 | 209 | 0.1948 | 3710 | 3919 | 96 | 1.967-1.9993 | 0.2115 | 192 | 0.1819 | 3664 | 3856 | 96 | 1.9993-2.0337 | 0.2217 | 181 | 0.182 | 3724 | 3905 | 97 | 2.0337-2.0707 | 0.2187 | 192 | 0.1831 | 3695 | 3887 | 97 | 2.0707-2.1105 | 0.22 | 218 | 0.176 | 3692 | 3910 | 97 | 2.1105-2.1536 | 0.1915 | 196 | 0.166 | 3659 | 3855 | 97 | 2.1536-2.2004 | 0.1802 | 217 | 0.1679 | 3720 | 3937 | 97 | 2.2004-2.2516 | 0.2117 | 179 | 0.1722 | 3667 | 3846 | 97 | 2.2516-2.3079 | 0.1871 | 188 | 0.1643 | 3759 | 3947 | 97 | 2.3079-2.3703 | 0.2 | 207 | 0.1637 | 3716 | 3923 | 97 | 2.3703-2.44 | 0.2013 | 193 | 0.1619 | 3719 | 3912 | 98 | 2.44-2.5187 | 0.2095 | 193 | 0.1586 | 3729 | 3922 | 98 | 2.5187-2.6087 | 0.1782 | 205 | 0.1676 | 3778 | 3983 | 98 | 2.6087-2.7131 | 0.2288 | 194 | 0.1764 | 3739 | 3933 | 98 | 2.7131-2.8366 | 0.2089 | 210 | 0.1772 | 3708 | 3918 | 98 | 2.8366-2.986 | 0.1901 | 212 | 0.1808 | 3728 | 3940 | 98 | 2.986-3.173 | 0.2017 | 192 | 0.1803 | 3799 | 3991 | 99 | 3.173-3.4178 | 0.206 | 214 | 0.1742 | 3721 | 3935 | 99 | 3.4178-3.7613 | 0.1884 | 203 | 0.1614 | 3800 | 4003 | 99 | 3.7613-4.3046 | 0.1672 | 210 | 0.148 | 3741 | 3951 | 99 | 4.3046-5.4198 | 0.1606 | 185 | 0.1337 | 3813 | 3998 | 99 | 5.4198-33.9279 | 0.1648 | 225 | 0.1617 | 3668 | 3893 | 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 | 2.2178 | -1.072 | 0.1617 | 1.1345 | -0.2749 | 0.8464 | -0.0813 | -0.2539 | -0.0901 | 0.1547 | 0.0317 | 0.1033 | -0.0065 | -0.0554 | 0.0473 | 0.1895 | -0.0102 | 0.0271 | 0.236 | -0.0047 | 0.163 | 43.7043 | 1.6607 | 3.2641 | 2 | 0.4099 | 0.7534 | -0.1367 | 2.0926 | 0.2612 | 0.8353 | 0.064 | -0.1408 | 0.0108 | 0.156 | -0.0766 | -0.1329 | 0.0197 | 0.0945 | 0.0222 | 0.1332 | 0.0048 | -0.0265 | 0.2298 | 0.0194 | 0.2019 | 64.1803 | 6.8971 | -0.6433 | 3 | 1.4156 | 0.3577 | 0.1077 | 0.735 | -0.0143 | 0.8274 | -0.0039 | -0.0794 | 0.2098 | -0.0088 | -0.0557 | 0.0979 | -0.1197 | -0.0135 | 0.0692 | 0.1595 | 0.0056 | -0.0055 | 0.1643 | -0.0263 | 0.1694 | 47.9801 | 16.0657 | -11.184 | 4 | 2.2261 | 1.527 | 0.3656 | 5.0685 | -0.0329 | 2.1029 | 0.0208 | -0.1144 | -0.1209 | 0.3577 | 0.0869 | 0.1323 | -0.1214 | -0.1962 | -0.0437 | 0.3063 | -0.0161 | 0.0329 | 0.2128 | 0.0104 | 0.1763 | 44.8004 | 28.8447 | -36.3422 | 5 | 1.317 | 0.9361 | -0.8643 | 1.0821 | -0.599 | 1.7138 | 0.1471 | -0.2142 | 0.0164 | 0.2528 | -0.128 | -0.0869 | -0.1275 | 0.3085 | 0.0174 | 0.2731 | -0.0245 | -0.0437 | 0.2389 | -0.0055 | 0.1848 | 63.2939 | 35.2921 | -42.5976 | 6 | 1.0927 | 0.0452 | -0.2017 | 0.9177 | 0.2516 | 0.8471 | 0.0713 | -0.0862 | 0.2857 | 0.1008 | -0.0061 | -0.1084 | -0.2391 | 0.125 | -0.0708 | 0.2363 | -0.0432 | -0.0076 | 0.1694 | -0.0309 | 0.19 | 59.745 | 46.8694 | -51.5949 | 7 | 2.0919 | -0.4184 | 0.3612 | 1.9211 | 0.1594 | 1.9576 | 0.0366 | -0.1588 | -0.0267 | 0.3193 | -0.0236 | 0.2545 | -0.0764 | -0.319 | -0.0418 | 0.2012 | 0.0086 | 0.0564 | 0.171 | -0.0084 | 0.1857 | 37.831 | 31.2011 | -46.5107 | 8 | 0.9913 | 0.6111 | 0.0924 | 2.0079 | 0.4644 | 0.9641 | 0.0857 | 0.0015 | 0.2768 | 0.2428 | -0.0629 | 0.2841 | -0.2873 | -0.121 | -0.0082 | 0.3027 | 0.0335 | 0.0273 | 0.157 | 0.0016 | 0.2663 | 41.3261 | 51.2297 | -52.3597 | 9 | 2.357 | -2.1221 | 0.1487 | 6.503 | -0.6344 | 2.0621 | 0.0221 | 0.2451 | -0.1048 | -0.3572 | -0.0621 | 0.3297 | 0.2716 | 0.005 | 0.0452 | 0.3131 | 0.0286 | 0.019 | 0.2354 | 0.0162 | 0.173 | 44.0682 | -0.1288 | -36.6717 | 10 | 2.5319 | -1.8033 | 1.7435 | 1.7045 | -1.2536 | 1.6956 | 0.1982 | 0.266 | 0.0055 | -0.5048 | -0.2986 | -0.192 | 0.4318 | 0.387 | 0.0548 | 0.3409 | 0.098 | 0.1085 | 0.2818 | 0.0443 | 0.1806 | 62.0046 | -7.1121 | -29.6353 | 11 | 1.2894 | -0.1235 | 0.1031 | 0.7692 | 0.0623 | 0.899 | 0.0141 | 0.1158 | -0.2298 | -0.2166 | -0.0535 | -0.1232 | 0.4241 | 0.1489 | 0.0143 | 0.3589 | 0.0673 | 0.0425 | 0.187 | 0.0077 | 0.1925 | 59.7679 | -21.2017 | -18.0688 | 12 | 0.7377 | -0.1806 | -0.3771 | 2.0565 | -0.2439 | 1.4494 | 0.0071 | 0.1206 | -0.0384 | -0.2407 | -0.0731 | 0.2225 | 0.1999 | -0.1089 | 0.0366 | 0.2339 | 0.0053 | -0.0185 | 0.1799 | -0.0179 | 0.1496 | 40.4361 | -2.6384 | -26.2372 | 13 | 1.323 | -0.7922 | 0.908 | 0.543 | -0.5123 | 0.7756 | 0.3324 | 0.0214 | -0.2629 | -0.3293 | -0.0007 | 0.064 | 0.7748 | -0.1709 | -0.0684 | 0.6982 | -0.0272 | -0.031 | 0.2928 | -0.0326 | 0.3129 | 41.3532 | -30.1779 | -28.2015 | 14 | 0.6417 | -0.0048 | -0.0301 | 1.2692 | 0.1991 | 0.4996 | 0.1415 | 0.0131 | -0.1317 | -0.1238 | -0.1107 | -0.0536 | 0.4238 | 0.0042 | -0.0298 | 0.3848 | 0.0008 | -0.0195 | 0.1664 | -0.0096 | 0.1837 | 44.4131 | -21.1409 | -19.3753 | 15 | 1.1443 | 0.3777 | 0.1432 | 2.373 | 0.7051 | 1.1566 | 0.1878 | -0.1538 | -0.0513 | 0.0437 | -0.1862 | 0.3387 | 0.3909 | -0.2038 | -0.0272 | 0.3597 | -0.1216 | 0.0016 | 0.24 | -0.0119 | 0.2237 | 33.564 | -19.1742 | -16.1325 | 16 | 0.2976 | 0.0502 | -0.011 | 0.8206 | -0.114 | 1.0199 | 0.0091 | 0.1002 | 0.0503 | -0.0743 | 0.0039 | 0.095 | 0.0229 | -0.084 | 0.0046 | 0.1253 | -0.0092 | -0.0084 | 0.1852 | 0.0072 | 0.1532 | 48.4223 | 27.9895 | -73.9767 | 17 | 1.6238 | -0.447 | -0.88 | 3.3651 | 1.2306 | 2.7453 | 0.0779 | -0.0429 | -0.0987 | -0.3756 | 0.0178 | -0.0685 | 0.0203 | 0.0996 | -0.1053 | 0.1998 | 0.0417 | -0.0061 | 0.218 | 0.0048 | 0.1985 | 68.1867 | 12.4913 | -77.2792 | 18 | 1.1339 | -0.0446 | -0.4131 | 0.6692 | 0.0883 | 0.803 | -0.0448 | 0.1014 | -0.0345 | -0.0077 | 0.0174 | 0.0744 | -0.0021 | -0.035 | 0.0214 | 0.0931 | -0.0077 | -0.0091 | 0.1529 | 0.0037 | 0.1256 | 50.2219 | 27.5992 | -66.9192 | 19 | 1.9321 | -0.8193 | -0.6603 | 1.1981 | 0.581 | 1.199 | -0.0042 | 0.0919 | -0.2325 | 0.0229 | -0.0435 | 0.0396 | 0.107 | 0.0621 | 0.0465 | 0.1799 | 0.0076 | -0.0014 | 0.1773 | -0.0094 | 0.1709 | 55.3223 | 10.6005 | -62.8783 | 20 | 2.9396 | 0.4881 | 0.1897 | 2.8687 | 0.5112 | 3.284 | -0.0439 | 0.0012 | -0.4362 | 0.2163 | 0.1264 | 0.046 | 0.5155 | -0.0059 | 0.0596 | 0.2638 | -0.0122 | 0.0099 | 0.1386 | 0.0144 | 0.2178 | 49.2942 | 5.5868 | -55.6659 |
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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 12 through 81 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 82 through 167 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 168 through 328 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 13 through 35 )B0 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 36 through 81 )B0 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 82 through 183 )B0 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 184 through 230 )B0 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 231 through 328 )B0 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 13 through 35 )C0 | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 36 through 81 )C0 | 11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 82 through 167 )C0 | 12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 168 through 236 )C0 | 13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 237 through 256 )C | | | | | | | | | | | | | | | | | | | | | | | | | |
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