ソフトウェア 名称 バージョン 分類 NB DENZOデータ削減 Show SCALEPACKデータスケーリング Show PHASER位相決定 Show RESOLVE位相決定 Show PHENIX1.8.1_1168精密化 Show PDB_EXTRACT3.11 データ抽出 Show
精密化 構造決定の手法 : 分子置換 / 解像度 : 2.806→38.639 Å / Occupancy max : 1 / Occupancy min : 0.43 / FOM work R set : 0.6818 / SU ML : 0.43 / σ(F) : 1.34 / 位相誤差 : 36.33 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.2952 1374 9.99 % Rwork 0.2458 - - obs 0.2507 13752 94.44 %
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 max : 147.47 Å2 / Biso mean : 74.7266 Å2 / Biso min : 32.87 Å2 精密化ステップ サイクル : LAST / 解像度 : 2.806→38.639 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2754 0 12 8 2774
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.004 2801 X-RAY DIFFRACTION f_angle_d0.854 3827 X-RAY DIFFRACTION f_chiral_restr0.041 512 X-RAY DIFFRACTION f_plane_restr0.005 485 X-RAY DIFFRACTION f_dihedral_angle_d17.677 983
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 10
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.8064-2.9067 0.3942 91 0.307 824 915 64 2.9067-3.023 0.4306 126 0.3115 1122 1248 87 3.023-3.1605 0.3685 138 0.3065 1260 1398 97 3.1605-3.3271 0.3202 139 0.2782 1260 1399 99 3.3271-3.5354 0.3534 143 0.2602 1288 1431 99 3.5354-3.8082 0.2971 143 0.2531 1293 1436 100 3.8082-4.191 0.2987 145 0.2256 1294 1439 99 4.191-4.7965 0.2574 145 0.1988 1314 1459 99 4.7965-6.0393 0.2971 148 0.2442 1324 1472 100 6.0393-38.6423 0.2551 156 0.2483 1399 1555 100
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 14) 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 4.0394 -0.0313 1.1609 2.4644 -1.4436 2.1002 0.2653 -0.0776 -0.4625 -1.6211 -0.0737 0.5813 0.6091 0.8965 -0.1546 0.5556 0.0127 0.1147 0.5295 -0.0133 0.2646 15.182 31.4875 -15.3097 2 -0.4582 -0.2488 -0.66 2.048 6.796 4.5184 0.6141 2.6769 0.0638 -1.8743 0.6469 -0.2229 -0.6219 0.0983 -0.654 1.188 0.0325 -0.0421 0.8294 0.3125 0.9997 12.826 57.2546 -18.4756 3 1.6579 -0.3976 2.0819 2.4597 -0.1569 2.4512 -0.5481 -0.1058 -0.8136 -0.3901 0.9566 0.002 -0.5402 -0.5389 0.0835 1.131 0.0782 0.0542 1.0717 0.3824 1.0323 15.185 74.0293 -20.4369 4 1.2592 3.0887 -2.0609 5.3507 -4.4043 3.2242 0.1738 0.1257 1.1608 -0.1314 0.8096 0.6823 -0.2893 1.0396 -0.5372 0.882 -0.0722 0.1512 0.6674 0.0106 0.8643 21.9075 62.4711 -17.0286 5 0.232 0.0573 -0.6071 5.1652 1.1224 2.0727 -0.07 0.0874 0.3786 -0.5158 0.1125 0.122 0.0824 0.1247 -0.081 0.3678 0.0586 -0.0687 0.3844 0.0205 0.4512 12.2322 42.9389 -9.0132 6 3.5198 -0.2657 -2.1688 0.2058 0.2865 2.1613 0.347 0.1439 -0.933 -0.46 0.1003 0.2202 1.2855 -0.4277 -0.346 0.9897 0.0065 -0.2099 0.4526 0.134 0.6361 -1.0373 32.5489 -18.7048 7 2.8545 0.3186 0.9599 4.8589 1.2091 3.0919 -0.089 -0.1929 0.6463 -0.5431 -0.2887 0.2855 -0.0857 0.0148 0.3221 0.4127 -0.0104 0.04 0.4309 0.0065 0.4447 12.151 52.2999 -8.2036 8 6.2988 0.1471 -0.7705 5.1052 0.2666 5.6773 -0.2973 0.3261 -0.4401 -1.2492 0.0141 0.7025 0.569 -0.5466 0.4804 0.7496 -0.043 -0.1994 0.4063 -0.0204 0.7311 2.4464 20.3565 -14.2139 9 3.5995 -1.6804 0.4022 4.4309 -0.2691 0.682 -0.2031 0.2417 0.6544 0.0301 -0.0464 -0.9567 0.0087 0.1787 0.0872 0.4664 0.0344 -0.062 0.5678 -0.0291 0.4982 24.3885 1.4007 -11.9571 10 0.4951 -0.7503 -0.5566 1.2232 0.37 0.3215 0.2317 0.2855 1.0597 1.8881 -0.0064 -0.0864 0.7291 0.6359 0.002 1.4435 0.3486 -0.0763 0.9081 0.007 0.9377 43.369 -27.4112 -8.6997 11 5.9296 -3.0942 -0.3886 4.5354 -0.2 3.2382 1.0091 1.062 0.2574 -1.8919 -0.956 0.0748 0.3284 -0.0578 0.0756 0.8628 -0.0366 -0.4413 0.3309 -0.0848 0.3961 19.7112 -1.038 -17.5599 12 2.6291 -1.3289 -0.0641 5.3045 -0.456 3.4438 0.2511 0.614 -0.1802 -0.5432 -0.0075 -0.1751 0.1454 0.3942 -0.1457 0.4357 0.056 -0.1114 0.4754 -0.1146 0.4353 24.5522 -7.1318 -16.8706 13 0.3423 0.3424 -1.1932 0.1072 -0.4251 4.356 -1.3776 0.7468 0.0436 0.9626 0.7775 1.5398 -1.6568 -2.1878 -0.3501 0.8567 0.4499 0.2086 0.8208 0.0363 0.7311 2.9033 5.0699 1.6672 14 2.1654 -1.8781 -0.0416 2.8489 -0.5902 0.8703 0.1055 0.2591 -0.4473 -0.629 -0.2362 0.3321 0.2793 -0.0932 -0.0205 0.7889 0.1132 -0.1094 0.5311 0.0009 0.5882 17.7386 -4.1973 -13.774
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'B' and (resid 43 through 69 )B0 2 X-RAY DIFFRACTION 2 chain 'B' and (resid 70 through 89 )B0 3 X-RAY DIFFRACTION 3 chain 'B' and (resid 90 through 99 )B0 4 X-RAY DIFFRACTION 4 chain 'B' and (resid 100 through 111 )B0 5 X-RAY DIFFRACTION 5 chain 'B' and (resid 112 through 165 )B0 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 166 through 182 )B0 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 183 through 231 )B0 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 232 through 254 )B0 9 X-RAY DIFFRACTION 9 chain 'A' and (resid 43 through 91 )A0 10 X-RAY DIFFRACTION 10 chain 'A' and (resid 92 through 106 )A0 11 X-RAY DIFFRACTION 11 chain 'A' and (resid 107 through 127 )A0 12 X-RAY DIFFRACTION 12 chain 'A' and (resid 128 through 167 )A0 13 X-RAY DIFFRACTION 13 chain 'A' and (resid 168 through 176 )A