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 REFMACrefmac_5.5.0047精密化 Show PDB_EXTRACT3.006 データ抽出 Show Blu-Iceデータ収集 HKL-2000データ削減 HKL-2000データスケーリング
精密化 構造決定の手法 : 分子置換開始モデル : 2qt8解像度 : 2.27→50 Å / Cor.coef. Fo :Fc : 0.94 / Cor.coef. Fo :Fc free : 0.904 / WRfactor Rfree : 0.236 / WRfactor Rwork : 0.181 / Occupancy max : 1 / Occupancy min : 0.4 / SU B : 12.257 / SU ML : 0.14 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.278 / ESU R Free : 0.225 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES : RESIDUAL ONLYRfactor 反射数 %反射 Selection details Rfree 0.245 1735 5 % RANDOM Rwork 0.188 - - - obs 0.191 34744 96.68 % -
溶媒の処理 イオンプローブ半径 : 0.8 Å / 減衰半径 : 0.8 Å / VDWプローブ半径 : 1.2 Å / 溶媒モデル : BABINET MODEL WITH MASK原子変位パラメータ Biso max : 86.47 Å2 / Biso mean : 27.895 Å2 / Biso min : 3.07 Å2 Baniso -1 Baniso -2 Baniso -3 1- 3.54 Å2 0 Å2 0 Å2 2- - -0.65 Å2 0 Å2 3- - - -2.9 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.27→50 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4654 0 38 307 4999
拘束条件 大きな表を表示 (5 x 16) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.008 0.022 4921 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 3462 X-RAY DIFFRACTION r_angle_refined_deg1.019 1.931 6659 X-RAY DIFFRACTION r_angle_other_deg0.993 3 8303 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.094 5 582 X-RAY DIFFRACTION r_dihedral_angle_2_deg31.81 23.148 270 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.035 15 770 X-RAY DIFFRACTION r_dihedral_angle_4_deg12.86 15 39 X-RAY DIFFRACTION r_chiral_restr0.064 0.2 644 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.021 5561 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 1150 X-RAY DIFFRACTION r_mcbond_it1.272 4 2859 X-RAY DIFFRACTION r_mcbond_other0.349 4 1173 X-RAY DIFFRACTION r_mcangle_it2.098 6 4590 X-RAY DIFFRACTION r_scbond_it2.571 6 2062 X-RAY DIFFRACTION r_scangle_it3.743 10 2061
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 20
大きな表を表示 (7 x 20) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.272-2.331 0.244 125 0.18 2100 2606 85.38 2.331-2.395 0.209 120 0.168 2180 2533 90.801 2.395-2.464 0.24 108 0.17 2235 2479 94.514 2.464-2.54 0.229 116 0.169 2266 2439 97.663 2.54-2.623 0.239 113 0.194 2174 2327 98.281 2.623-2.715 0.375 118 0.303 2049 2276 95.211 2.715-2.818 0.241 112 0.165 2051 2180 99.22 2.818-2.933 0.207 99 0.163 2003 2117 99.291 2.933-3.063 0.272 99 0.171 1915 2024 99.506 3.063-3.212 0.248 93 0.176 1826 1927 99.585 3.212-3.386 0.231 82 0.193 1772 1859 99.731 3.386-3.591 0.301 77 0.218 1636 1746 98.11 3.591-3.838 0.242 74 0.208 1557 1684 96.853 3.838-4.145 0.238 76 0.19 1388 1541 95.003 4.145-4.54 0.248 76 0.152 1355 1432 99.93 4.54-5.074 0.188 55 0.152 1263 1320 99.848 5.074-5.856 0.218 70 0.17 1089 1160 99.914 5.856-7.165 0.256 57 0.201 948 1006 99.901 7.165-10.103 0.2 43 0.18 750 793 100 10.103-92.45 0.285 22 0.255 452 487 97.331
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 16) 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 5.4035 -0.305 -0.8866 2.0851 -0.4581 1.8351 -0.0047 0.3435 -0.3668 -0.3324 -0.0184 0.2989 0.4322 -0.0629 0.0231 0.4003 -0.0712 -0.0541 0.1205 -0.0241 0.2231 49.527 43.764 28.947 2 4.2175 -0.2889 -1.7361 2.0013 0.3342 7.2375 0.0545 0.4387 -0.2125 -0.4181 -0.0674 0.3794 0.2145 -0.0978 0.0129 0.3594 -0.1063 -0.1175 0.1312 -0.0062 0.1841 44.077 50.479 26.463 3 6.096 0.9798 -0.2857 5.0986 -1.2438 9.3847 -0.3051 1.341 0.379 -0.6122 0.2068 -0.6059 0.4417 0.981 0.0983 0.4087 -0.0621 0.0409 0.4732 0.0283 0.1634 61.567 48.471 17.746 4 5.5373 -2.7831 -2.2427 2.8976 1.6171 2.7545 0.0954 0.3192 -0.0613 -0.2434 -0.0744 0.0567 0.1982 -0.0049 -0.021 0.2895 -0.0517 -0.04 0.179 0.0376 0.1798 52.303 54.175 32.023 5 12.5006 0.3844 0.3046 4.3552 5.0633 19.9636 -0.7293 1.0262 -0.8345 0.0011 0.28 -0.0787 0.7803 0.2673 0.4493 0.3776 0.0325 0.1847 0.6081 -0.024 0.5322 77.311 46.463 17.801 6 0.7006 -0.5175 0.1559 1.357 -0.2538 0.7853 -0.0201 -0.027 -0.0642 0.0066 0.0091 -0.0403 0.094 0.1084 0.011 0.2212 -0.0207 0.0001 0.1517 0.017 0.1508 59.526 56.183 40.893 7 2.0977 0.1868 -0.9671 2.3784 -0.9397 2.8127 0.0895 -0.1041 -0.0232 0.0053 -0.039 0.3 0.0233 -0.1103 -0.0505 0.2241 -0.0476 -0.0275 0.1766 0.0063 0.2042 42.172 65.34 37.887 8 1.0276 -0.0039 0.4336 1.1435 -0.3508 2.0765 0.0106 0.0543 -0.0402 -0.0268 0.0129 0.0791 0.1904 0.0522 -0.0235 0.2182 -0.0291 -0.013 0.1549 0.0047 0.1981 47.298 68.24 36.794 9 6.1279 -3.3855 2.475 12.129 1.8551 2.0933 -0.2408 0.5372 -0.0029 -0.4947 0.2724 -0.6062 -0.3394 0.5502 -0.0316 0.3811 -0.1336 -0.0113 0.5944 0.0826 0.4312 55.394 106.255 15.843 10 2.4256 1.2843 -0.7304 2.2635 -0.0222 2.6003 0.067 -0.1786 0.288 0.2196 -0.0078 0.2758 -0.2119 -0.2654 -0.0592 0.1476 0.04 0.0325 0.2257 -0.0165 0.215 36 95.655 23.81 11 1.3182 0.5233 1.9211 1.3185 0.651 3.0599 -0.0816 0.1298 -0.0895 0.0304 0.0872 -0.1776 -0.1434 0.4091 -0.0056 0.218 0.0202 0.0323 0.3129 -0.0194 0.2165 48.139 91.973 26.694 12 1.1312 1.0557 -0.3333 2.087 -0.4195 1.259 0.1168 -0.0976 -0.0271 0.1058 -0.0732 0.049 0.032 0.0282 -0.0436 0.1541 -0.0022 -0.0119 0.2407 0.0037 0.1882 41.307 85.918 18.31 13 10.3285 2.3662 -2.2844 4.6763 -1.8967 4.6017 0.2789 -0.5806 0.4658 0.1209 -0.3281 -0.7647 -0.394 0.9688 0.0492 0.1897 -0.0367 0.0116 0.3517 0.0353 0.2331 60.407 97.229 11.714 14 0.5846 0.1628 0.0524 1.0668 -0.2709 1.019 0.06 0.0666 -0.0164 -0.1259 0.0128 0.1247 0.1019 -0.1349 -0.0728 0.1585 0.0002 -0.028 0.208 0.0074 0.1886 38.967 81.987 10.399 15 2.8926 -0.5116 1.2222 3.1141 4.9303 10.8935 0.0089 -0.0118 0.1867 -0.0138 0.3891 -0.6627 -0.4484 1.0523 -0.398 0.3484 -0.0957 -0.0511 0.3506 0.0215 0.4197 54.736 80.699 23.729 16 1.043 -0.6163 1.0154 0.6599 -0.4788 2.9909 0.0729 0.0975 -0.0739 -0.1693 0.0216 0.2112 0.1532 -0.1814 -0.0945 0.2118 -0.0542 -0.0429 0.1954 0.0025 0.2102 36.345 69.47 15.098
精密化 TLSグループ 大きな表を表示 (7 x 16) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA3 - 39 8 - 44 2 X-RAY DIFFRACTION 2 AA40 - 61 45 - 66 3 X-RAY DIFFRACTION 3 AA62 - 86 67 - 91 4 X-RAY DIFFRACTION 4 AA87 - 114 92 - 119 5 X-RAY DIFFRACTION 5 AA115 - 122 120 - 127 6 X-RAY DIFFRACTION 6 AA123 - 219 128 - 224 7 X-RAY DIFFRACTION 7 AA220 - 251 225 - 256 8 X-RAY DIFFRACTION 8 AA252 - 301 257 - 306 9 X-RAY DIFFRACTION 9 BB1 - 6 6 - 11 10 X-RAY DIFFRACTION 10 BB7 - 36 12 - 41 11 X-RAY DIFFRACTION 11 BB37 - 88 42 - 93 12 X-RAY DIFFRACTION 12 BB89 - 114 94 - 119 13 X-RAY DIFFRACTION 13 BB115 - 129 120 - 134 14 X-RAY DIFFRACTION 14 BB130 - 247 135 - 252 15 X-RAY DIFFRACTION 15 BB248 - 261 253 - 266 16 X-RAY DIFFRACTION 16 BB262 - 301 267 - 306