ソフトウェア 名称 バージョン 分類 PHENIX(1.11.1_2575: ???)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
精密化 構造決定の手法 : 分子置換開始モデル : 3RVY, tetramer解像度 : 3.198→29.963 Å / 交差検証法 : FREE R-VALUE / σ(F) : 153.12 / 位相誤差 : 24.1 Rfactor 反射数 %反射 Rfree 0.2459 2002 3.9 % Rwork 0.2124 - - obs 0.2175 51426 99.76 %
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å精密化ステップ サイクル : LAST / 解像度 : 3.198→29.963 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 6850 0 356 0 7206
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.003 7404 X-RAY DIFFRACTION f_angle_d0.544 10086 X-RAY DIFFRACTION f_dihedral_angle_d13.146 4179 X-RAY DIFFRACTION f_chiral_restr0.04 1192 X-RAY DIFFRACTION f_plane_restr0.004 1164
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 (%)3.1988-3.2787 0.2905 142 0.2624 3409 X-RAY DIFFRACTION 94 3.2787-3.3673 0.2784 138 0.2422 3510 X-RAY DIFFRACTION 96 3.3673-3.4662 0.2643 142 0.2371 3467 X-RAY DIFFRACTION 96 3.4662-3.5779 0.2424 139 0.2269 3496 X-RAY DIFFRACTION 96 3.5779-3.7056 0.2533 145 0.2242 3519 X-RAY DIFFRACTION 96 3.7056-3.8536 0.2361 140 0.2186 3499 X-RAY DIFFRACTION 96 3.8536-4.0286 0.2252 139 0.2035 3492 X-RAY DIFFRACTION 96 4.0286-4.2404 0.2224 145 0.2075 3501 X-RAY DIFFRACTION 96 4.2404-4.5053 0.2955 146 0.2078 3546 X-RAY DIFFRACTION 96 4.5053-4.8518 0.2163 142 0.1908 3527 X-RAY DIFFRACTION 96 4.8518-5.3375 0.2683 144 0.2 3539 X-RAY DIFFRACTION 96 5.3375-6.104 0.2547 145 0.2292 3566 X-RAY DIFFRACTION 96 6.104-7.6685 0.2849 145 0.2313 3610 X-RAY DIFFRACTION 96 7.6685-29.7363 0.2168 150 0.2128 3734 X-RAY DIFFRACTION 96
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 24) 大きな表を隠す 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)1 0.2026 -0.6171 0.212 2.0613 -0.0711 2.0341 0.1663 -0.0699 -0.1391 0.7314 0.135 0.5561 0.1098 -0.7515 -0.3183 1.542 -0.3783 0.1538 1.4497 0.6621 1.1547 90.51 130.4453 44.7952 2 1.5071 -0.139 0.3829 3.3302 -0.019 0.9102 -0.1862 -0.4376 -0.6221 0.6778 0.2009 0.6351 0.5448 -0.5811 0.1074 0.9511 -0.3711 -0.0517 0.9365 0.4874 1.0906 102.6612 129.5399 29.0363 3 1.3319 0.7217 -0.0983 1.0194 -0.4085 0.2081 0.0548 -0.1603 -0.5272 -0.2459 0.2629 0.2227 0.0688 -0.572 -0.2872 0.9933 -0.3192 -0.0326 1.0371 0.4936 1.2176 96.1862 132.2643 24.2522 4 7.5628 3.2103 0.4486 3.1933 -0.3399 0.1803 0.3243 -0.5138 -0.008 0.6162 -0.2592 0.194 -0.2064 -0.1269 -0.1043 1.0001 -0.0014 0.4189 1.2247 0.4609 0.9133 95.2657 143.8026 32.7062 5 3.751 0.3096 -1.024 3.8965 1.8057 1.2025 -0.0862 0.6211 0.0949 -0.2838 0.16 0.6757 0.3018 -1.1685 -0.5914 0.8241 -0.1594 0.1102 1.2698 0.5514 0.9196 99.0352 140.7684 22.2227 6 0.8139 -0.3619 0.5999 0.4484 0.0012 0.7129 0.1834 -0.5455 0.0886 0.1969 0.067 0.0514 0.1279 -0.1104 0.516 0.6561 -0.0689 0.127 0.7861 -0.1765 0.1865 116.9007 167.2704 21.1246 7 1.2752 -0.4274 0.4857 5.152 -6.1704 8.9216 -0.0406 -0.7547 -0.3153 0.2231 0.0087 -0.2604 0.4294 0.4477 0.0444 0.8637 0.184 -0.1432 1.2202 0.1981 0.6703 156.1971 128.8983 31.3485 8 1.6176 -0.2748 0.536 2.2033 0.5679 0.4171 0.2639 -0.2461 -0.6309 -0.1161 0.512 0.1349 0.487 -0.4561 -0.675 1.061 0.2538 -0.3809 1.1504 0.1977 0.9331 152.5714 126.8774 22.082 9 1.6052 -0.0948 -1.9618 0.2469 0.273 2.5006 -0.0045 -0.2606 -0.2458 0.2797 0.2237 0.1289 0.3249 0.0947 -0.1064 1.0238 0.0462 -0.3351 1.1131 0.5003 0.9209 141.8891 126.1914 29.1218 10 4.4316 0.0064 0.6541 3.2175 -1.6427 1.4213 0.1846 0.4153 -0.2125 -0.5704 0.0184 0.1073 0.8968 0.1282 -0.4492 1.0726 0.0259 -0.1861 1.174 0.5566 0.7971 144.1645 129.6421 20.1647 11 0.1881 -0.4676 0.1184 1.2827 -0.6888 1.2533 0.0902 -0.3549 -0.3384 0.2715 0.0332 0.0458 0.2157 0.0243 -0.2298 0.6137 -0.0892 -0.0371 0.7459 0.2354 0.2614 119.7938 144.4189 20.6899 12 0.3794 0.0583 0.5888 0.2461 0.3657 1.2338 0.0436 0.1232 0.0307 -0.0068 0.0657 0.0632 -0.2196 -0.1941 -0.0656 0.4685 -0.1003 0.0333 0.6824 0.1441 0.2044 108.6192 156.1063 7.6851 13 0.247 -0.2494 0.1962 0.765 -0.1794 1.6157 -0.0411 -0.252 -0.0345 0.4824 0.018 -0.0589 -0.0741 0.3014 0.2154 0.7679 -0.0873 0.0528 0.9482 0.2156 0.2785 116.358 153.4972 27.3499 14 2.8987 0.0834 3.8951 0.9846 0.6557 5.5331 -0.441 -0.0135 0.6873 0.4604 0.087 -0.2261 -0.609 0.4927 0.5045 1.1537 -0.4002 0.0256 1.119 -0.4252 0.8787 154.8023 185.9593 26.742 15 1.7645 1.3833 -0.1137 1.3479 0.1664 0.5759 0.1772 0.2689 0.0181 0.1546 0.2094 -0.1633 0.2493 0.2549 0.1921 0.6608 -0.2519 -0.0079 1.4147 -0.5796 0.9012 161.4094 178.3034 27.9414 16 5.2399 0.2393 1.8654 5.458 -0.4459 0.7158 -0.0799 0.7874 0.0602 -0.2223 0.0798 -0.6769 -0.4189 0.7711 -0.1382 0.6348 -0.2416 -0.1757 1.0413 -0.3041 0.7164 155.1599 174.8793 20.3 17 0.3235 0.1196 0.6589 0.1567 0.3217 1.3991 0.1886 -0.4098 -0.076 0.249 -0.0826 -0.0874 -0.21 -0.0842 -0.2843 0.7045 -0.0509 -0.1211 1.1883 -0.0086 0.3513 143.7292 152.8697 27.8157 18 1.3608 -0.0531 1.1921 0.9075 -0.34 1.5047 0.1203 -0.112 -0.2048 0.1874 -0.0253 -0.0528 0.0791 -0.0206 -0.1392 0.4871 0.0231 -0.184 0.5961 0.1527 0.2496 133.9789 146.4697 15.9008 19 0.1905 0.3563 0.5953 2.5553 2.147 2.4247 0.3633 -0.0771 0.6529 0.0745 -0.2517 0.4661 -0.3593 -0.2913 0.1472 0.8841 0.1882 0.2267 1.4869 -0.2719 0.6644 98.9436 185.6894 28.8146 20 0.3946 -0.5925 0.0524 1.0439 0.1044 0.2116 -0.1067 -0.1875 -0.1038 0.0268 0.0128 0.2503 -0.0507 0.0143 0.7665 0.9568 0.1933 0.4115 1.0685 -0.4088 0.9585 107.0317 191.3973 30.38 21 0.4495 -0.0148 -0.2669 4.1234 0.0194 0.2658 0.0842 1.0361 0.4915 -1.4428 -0.0108 0.1898 -0.5498 -0.318 -0.0808 0.8888 -0.0784 -0.0268 1.1713 -0.3677 0.9303 111.7447 189.9484 15.0957 22 0.1715 -0.082 0.1479 0.1631 0.028 0.1949 -0.1533 -0.3072 0.0427 0.2817 0.0106 0.1414 -0.0967 -0.1336 -0.2389 0.7645 -0.128 0.1335 1.0025 -0.3291 0.4082 127.2702 175.8436 28.603 23 2.4513 -2.2847 -2.1325 3.5382 3.1263 3.3021 0.4976 0.192 0.3249 -0.7717 0.0409 -0.2233 -1.0018 0.2912 -0.2575 0.6808 -0.0478 -0.0056 0.4553 -0.0931 0.1996 140.1712 171.6035 4.509 24 0.0622 -0.0345 0.1152 0.3367 0.0858 0.2863 0.0215 -0.193 0.0793 0.0021 0.0278 0.0147 0.1776 0.019 0.0254 0.4947 -0.0683 -0.0056 0.8457 -0.2109 0.1823 138.2618 163.6846 17.5342
精密化 TLSグループ 大きな表を表示 (4 x 24) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1002 through 1011 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 1012 through 1031 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 1032 through 1070 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 1071 through 1088 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 1089 through 1113 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 1114 through 1218 )7 X-RAY DIFFRACTION 7 chain 'B' and (resid 2001 through 2031 )8 X-RAY DIFFRACTION 8 chain 'B' and (resid 2032 through 2073 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 2074 through 2088 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 2089 through 2113 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 2114 through 2183 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 2184 through 2193 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 2194 through 2218 )14 X-RAY DIFFRACTION 14 chain 'C' and (resid 1001 through 1041 )15 X-RAY DIFFRACTION 15 chain 'C' and (resid 1042 through 1088 )16 X-RAY DIFFRACTION 16 chain 'C'