ソフトウェア 名称 バージョン 分類 PHENIX(PHENIX.REFINE: 1.8.2_1309)精密化 XDSデータ削減 XSCALEデータスケーリング PHASER位相決定
精密化 構造決定の手法 : 分子置換開始モデル : PDB ENTRY 1E8O CHAINS A AND B解像度 : 2.04→56.746 Å / SU ML : 0.26 / σ(F) : 2 / 位相誤差 : 23.13 / 立体化学のターゲット値 : ML詳細: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 78 TO 86. CHAIN B, RESIDUES 41 TO 48. CHAIN C, RESIDUES 68, 69. CHAIN D, RESIDUES 75 TO 86. CHAIN E, RESIDUES 41 TO 50. CHAIN F, ... 詳細 : THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 78 TO 86. CHAIN B, RESIDUES 41 TO 48. CHAIN C, RESIDUES 68, 69. CHAIN D, RESIDUES 75 TO 86. CHAIN E, RESIDUES 41 TO 50. CHAIN F, RESIDUES 57, 69. THE FOLLOWING RESIDUES WERE TRUNCATED AT THE CB POSITIONS. CHAIN A, RESIDUES 76, 77. CHAIN B, RESIDUE 50. MG ION COORDINATION WAS RESTRAINED. HYDROGENS WERE ADDED IN THE RIDING POSITIONS.Rfactor 反射数 %反射 Rfree 0.222 1539 3.1 % Rwork 0.1855 - - obs 0.1866 49531 99.35 %
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原子変位パラメータ Biso mean : 35.9 Å2 精密化ステップ サイクル : LAST / 解像度 : 2.04→56.746 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2557 3671 29 381 6638
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.003 6732 X-RAY DIFFRACTION f_angle_d0.723 9938 X-RAY DIFFRACTION f_dihedral_angle_d13.472 3039 X-RAY DIFFRACTION f_chiral_restr0.034 1244 X-RAY DIFFRACTION f_plane_restr0.003 601
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 (%)2.0401-2.1059 0.3305 128 0.2823 4272 X-RAY DIFFRACTION 98 2.1059-2.1812 0.3093 132 0.2634 4348 X-RAY DIFFRACTION 99 2.1812-2.2685 0.2642 141 0.2526 4375 X-RAY DIFFRACTION 99 2.2685-2.3718 0.2902 158 0.2447 4322 X-RAY DIFFRACTION 100 2.3718-2.4968 0.2872 148 0.23 4336 X-RAY DIFFRACTION 100 2.4968-2.6532 0.2438 127 0.2254 4331 X-RAY DIFFRACTION 100 2.6532-2.8581 0.2537 137 0.2123 4380 X-RAY DIFFRACTION 100 2.8581-3.1457 0.2274 151 0.1898 4390 X-RAY DIFFRACTION 100 3.1457-3.6008 0.1902 148 0.1566 4351 X-RAY DIFFRACTION 99 3.6008-4.5363 0.1872 138 0.1431 4404 X-RAY DIFFRACTION 99 4.5363-56.7676 0.1818 131 0.1604 4483 X-RAY DIFFRACTION 99
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 29) 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 1.0581 0.1896 0.7412 1.0678 0.4543 0.7945 0.2243 -0.1949 -0.1054 0.2499 0.0798 -0.2564 0.3314 -0.0943 0.659 0.258 -0.0991 -0.078 0.4413 -0.1235 0.3061 28.0401 -1.0122 34.7206 2 3.2189 -0.342 0.9744 0.9409 -1.9844 4.2027 -0.0874 -0.2589 0.6018 0.247 -0.1433 0.056 -1.003 0.2063 -0.6102 0.313 -0.0536 0.0901 0.1498 -0.0143 0.3533 20.482 5.4655 29.2256 3 0.0285 0.0031 0.0183 0.0446 0.0343 0.0354 -0.0373 0.6874 -0.2061 -0.2994 -0.2856 -0.1235 -0.2901 0.1206 0.0004 0.3326 0.0436 0.0389 0.273 0.0461 0.4077 16.4254 0.6156 16.6565 4 1.0033 0.1993 -0.312 0.8676 0.3658 0.4365 0.1626 -0.2173 0.0235 0.1752 -0.057 -0.1178 -0.095 0.3212 -0.0053 0.1665 0.0046 -0.0193 0.1815 -0.0221 0.1976 19.9001 -7.7166 33.0103 5 0.3465 0.4645 -0.4418 0.6706 -1.0148 4.4226 0.0228 -0.419 0.3731 0.3558 -0.0359 0.297 -0.5528 -0.9289 1.1709 0.2669 -0.0247 0.0459 0.3261 -0.1198 0.2678 11.0082 1.3426 33.4688 6 3.7296 4.8902 -6.5114 7.0152 -9.6891 2 0.0688 0.1733 0.1817 -0.3041 -0.0048 -0.1284 -0.4191 -0.0537 0.133 0.5792 0.0511 -0.0996 0.2279 0.0909 0.3845 5.5987 8.9019 17.3842 7 0.0049 -0.0341 -0.0673 1.1315 -0.1983 2.5528 0.0256 -0.2398 -0.3787 -0.0164 0.0462 0.4149 0.2787 -0.8639 -0.1619 0.1909 -0.0161 0.0249 0.2617 0.0224 0.2727 2.3443 -15.3516 32.3417 8 0.7823 0.1602 -0.1714 0.394 0.4263 0.8925 -0.0243 0.1074 -0.0598 0.0806 0.0175 0.2098 -0.004 -0.1339 -0.0976 0.1317 0.0476 -0.0037 0.1409 -0.0044 0.197 7.4367 -10.3441 25.331 9 0.6601 0.7578 0.1893 3.3077 -0.6463 0.3604 0.3579 0.3657 0.0132 -1.1337 -0.4926 -0.5989 0.1621 -0.1655 0.0278 0.3526 0.0877 0.0137 0.3027 0.0467 0.3706 7.9122 -7.0116 9.52 10 0.0243 -0.0311 -0.0651 0.0677 0.0507 0.2016 0.0494 0.146 0.0618 -0.1457 -0.0912 -0.0559 -0.0348 0.0207 0.3066 0.476 0.2443 -0.0116 0.4337 0.1394 0.3365 4.22 0.9915 10.8241 11 1.762 0.0109 -0.9621 1.955 -0.3275 0.5801 -0.2077 -0.4071 0.1813 0.5279 -0.1231 -0.0487 -0.3106 -0.2228 -0.7206 0.2238 0.047 0.0115 0.1687 -0.0091 0.2408 4.7937 -4.7737 37.4599 12 0.7967 0.1805 0.1166 1.3049 0.0633 0.963 -0.0305 0.1994 -0.2096 -0.0583 -0.0275 0.0167 0.2573 -0.1382 0.0177 0.16 0.0082 0.0221 0.1731 -0.0451 0.2437 15.5731 -26.8902 17.4699 13 0.4312 -0.3569 0.1912 0.3496 -0.0382 0.3312 0.1715 0.2732 0.7393 -0.1917 -0.0364 0.3845 -0.2236 0.0863 0.0009 0.3744 -0.0672 0.1019 0.3052 -0.0487 0.4525 21.4129 -37.0104 9.0565 14 1.5533 0.1562 -0.6674 1.7608 0.2321 1.4239 -0.1294 0.242 -0.1343 -0.1177 0.0128 -0.211 -0.0791 0.3081 -0.1131 0.1648 0.0255 0.0167 0.2395 -0.0008 0.2133 30.3371 -15.6943 13.5994 15 4.2256 -1.454 -1.9842 1.2736 -0.0498 3.3746 0.0705 -0.4495 0.7098 -0.3934 -0.3143 -0.1942 -1.3147 0.6714 0.6715 0.8172 -0.0121 -0.2466 0.6771 0.0185 0.4753 45.6326 -17.7233 38.8026 16 0.3881 -0.0824 -0.3009 0.5982 0.1669 0.2515 -0.4593 0.247 -0.0928 -0.2112 -0.2497 0.1193 -0.5182 -0.4634 -0.1026 0.757 0.0307 -0.1826 0.3276 0.0408 0.6248 51.7656 -3.4785 46.7611 17 0.2915 0.3471 -0.255 3.0992 0.8679 1.1515 -0.0146 -0.0154 0.3304 -0.8974 0.2553 0.0143 -0.2716 0.0393 0.2292 0.5026 -0.0283 -0.0408 0.2889 -0.091 1.1477 58.8212 3.0688 52.6291 18 0.0116 -0.0241 0.0275 0.0497 -0.0567 0.0645 0.0445 -0.2104 0.2985 0.044 0.0034 0.3562 -0.0342 -0.1404 0.1413 0.274 -0.0917 0.0366 0.6379 -0.2977 0.7396 61.2769 -0.4699 66.584 19 1.0425 -0.8691 0.337 1.1812 0.1083 0.4471 -0.1773 0.192 0.4739 -0.5069 -0.0782 0.3491 -0.1268 -0.1198 -0.2468 0.4454 -0.1126 -0.0529 0.2472 -0.0667 0.3981 59.5913 -10.3045 50.5591 20 0.2453 -0.0774 0.3094 0.3391 -0.0462 0.3976 -0.2186 0.305 0.6012 -0.434 -0.12 0.4164 -0.0454 0.4076 -0.0202 0.5328 -0.1305 0.0142 0.3232 0.0878 0.6124 68.7097 -1.2877 50.1394 21 1.1285 0.193 1.6473 1.4615 -0.6025 2.9558 -0.2327 -0.2573 -0.4003 -0.1579 0.2014 -0.7649 0.1074 0.808 -0.4327 0.2621 -0.0555 0.056 0.5768 -0.1449 0.3876 76.7872 -17.834 53.9426 22 0.2255 -0.2537 0.425 0.2912 -0.4842 0.7994 -0.066 -0.2991 0.2082 -0.0032 0.1612 -0.3332 -0.1565 0.3959 0.0606 0.3315 -0.1098 0.0391 0.3757 -0.1525 0.3104 71.1004 -12.1086 59.8973 23 0.145 0.0449 -0.0824 0.0135 -0.0253 0.0465 0.1327 -0.0708 -0.0546 -0.0248 0.0649 -0.0703 0.1662 0.1198 1.2283 0.398 -0.1356 -0.0585 0.6639 -0.2716 0.4446 68.7257 -7.4575 75.1557 24 0.0397 -0.0251 0.0176 0.016 -0.0111 0.0078 0.0174 0.0027 0.0251 -0.0177 0.0077 0.0691 0.0408 -0.0103 0.7906 1.0259 -0.3494 -0.243 0.7915 -0.3493 1.0383 72.7407 1.8097 70.9437 25 3.9328 -0.3066 2.7566 0.1648 0.0087 2.2866 -0.6369 0.4333 0.8442 -0.5826 0.0862 -0.188 -0.217 0.0517 -0.4158 0.6141 -0.2526 0.0544 0.4572 -0.0032 0.4705 74.9034 -7.6547 47.7324 26 0.8305 -0.833 -0.2512 1.0227 -0.2931 1.9369 -0.155 -0.6127 -0.053 0.0898 0.1201 -0.0756 0.2575 -0.0413 -0.0671 0.2942 -0.0566 0.0084 0.4523 -0.0346 0.1524 62.325 -28.2851 68.4132 27 1.6633 -1.4503 -0.8632 2.2718 0.5167 0.5037 0.1634 -0.3301 0.2035 0.0796 -0.08 -0.2379 -0.0527 -0.581 0.0767 0.4697 -0.0256 0.1061 0.8234 0.1477 0.3494 55.7083 -37.8025 76.7989 28 0.1952 0.5547 -0.1257 1.9721 0.1406 1.98 -0.1491 -0.5163 0.301 -0.0387 0.0174 0.359 -0.1379 -0.377 0.1655 0.3227 0.0425 -0.0388 0.7188 -0.1942 0.3233 47.3542 -16.5614 69.3623 29 7.8207 1.1996 -6.0837 2.3684 0.5817 7.9378 0.2243 -0.0013 1.6329 -0.1747 -0.159 0.5311 -1.9172 -0.6513 2.4473 0.9337 0.1342 -0.3407 0.6869 -0.016 0.6526 36.0876 -15.6457 42.1433
精密化 TLSグループ 大きな表を表示 (4 x 29) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 CHAIN 'A' AND (RESSEQ 2:6)2 X-RAY DIFFRACTION 2 CHAIN 'A' AND (RESSEQ 7:20)3 X-RAY DIFFRACTION 3 CHAIN 'A' AND (RESSEQ 21:25)4 X-RAY DIFFRACTION 4 CHAIN 'A' AND (RESSEQ 26:55)5 X-RAY DIFFRACTION 5 CHAIN 'A' AND (RESSEQ 56:74)6 X-RAY DIFFRACTION 6 CHAIN 'A' AND (RESSEQ 75:77)7 X-RAY DIFFRACTION 7 CHAIN 'B' AND (RESSEQ 2:22)8 X-RAY DIFFRACTION 8 CHAIN 'B' AND ((RESSEQ 23:32) OR (RESSEQ 55:75))9 X-RAY DIFFRACTION 9 CHAIN 'B' AND (RESSEQ 33:40)10 X-RAY DIFFRACTION 10 CHAIN 'B' AND (RESSEQ 49:54)11 X-RAY DIFFRACTION 11 CHAIN 'B' AND (RESSEQ 76:95)12 X-RAY DIFFRACTION 12 CHAIN 'C' AND ((RESSEQ 1:33) OR (RESSEQ 41:48))13 X-RAY DIFFRACTION 13 CHAIN 'C' AND (RESSEQ 34:40)14 X-RAY DIFFRACTION 14 CHAIN 'C' AND ((RESSEQ 49:64) OR (RESSEQ 102:118))15 X-RAY DIFFRACTION 15 CHAIN 'C' AND ((RESSEQ 65:69) OR (RESSEQ 99:101))16 X-RAY DIFFRACTION 16 CHAIN '