ソフトウェア 名称 バージョン 分類 NB XSCALEデータスケーリング Show PHASER位相決定 Show REFMAC5.6.0117精密化 Show PDB_EXTRACT3.004 データ抽出 Show XDSデータ削減
精密化 構造決定の手法 : 分子置換開始モデル : PDB ENTRY 3R9l解像度 : 2.3→50 Å / Cor.coef. Fo :Fc : 0.947 / Cor.coef. Fo :Fc free : 0.92 / SU B : 13.043 / SU ML : 0.164 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.32 / ESU R Free : 0.223 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.235 2144 5 % RANDOM Rwork 0.198 - - - obs 0.2 42483 98.92 % -
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 : MASK原子変位パラメータ Biso mean : 40.762 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.63 Å2 0 Å2 0 Å2 2- - -1.89 Å2 -0 Å2 3- - - 2.52 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.3→50 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 6311 0 3 286 6600
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.014 0.019 6442 X-RAY DIFFRACTION r_bond_other_d0.008 0.02 4316 X-RAY DIFFRACTION r_angle_refined_deg1.411 1.946 8728 X-RAY DIFFRACTION r_angle_other_deg1.232 3 10478 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.082 5 830 X-RAY DIFFRACTION r_dihedral_angle_2_deg28.429 23.384 263 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.369 15 1004 X-RAY DIFFRACTION r_dihedral_angle_4_deg24.369 15 42 X-RAY DIFFRACTION r_chiral_restr0.078 0.2 976 X-RAY DIFFRACTION r_gen_planes_refined0.009 0.021 7270 X-RAY DIFFRACTION r_gen_planes_other0.007 0.02 1364
LS精密化 シェル 解像度 : 2.3→2.36 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.323 131 - Rwork 0.262 2541 - all - 2672 - obs - - 92.3 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 18) 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 1.3902 -0.4413 0.1005 1.3394 -0.3089 0.548 0.0322 0.0803 -0.0713 -0.1244 0.056 -0.0159 -0.0546 -0.0195 -0.0882 0.1213 -0.0142 -0.0925 0.0884 0.0073 0.1509 -4.834 13.717 -31.964 2 7.4028 -1.6897 -2.7973 1.9782 -1.3931 9.5511 0.3817 0.23 0.6845 0.1313 0.3602 0.2143 -0.9947 -1.2989 -0.742 0.2512 0.1077 -0.0166 0.2142 0.1446 0.2748 -7.417 31.004 -32.628 3 1.4848 0.0627 -0.2104 1.422 -0.1652 1.3167 -0.0135 0.2269 0.1033 -0.2003 0.1184 0.2486 -0.0839 -0.089 -0.1049 0.1299 -0.0037 -0.135 0.1046 0.0248 0.1718 -10.518 13.107 -34.543 4 2.3091 -0.6298 -1.22 2.0441 0.725 3.7037 -0.009 -0.1022 -0.2182 0.1138 0.295 -0.1769 0.3899 -0.035 -0.2859 0.1421 0.0066 -0.1854 0.0637 -0.0494 0.3481 7.396 -13.866 -15.928 5 2.9227 -0.3464 -0.8463 1.8982 -0.3075 1.574 0.03 -0.2215 -0.4792 0.2192 0.0872 -0.1815 0.2108 0.2353 -0.1171 0.1407 0.0438 -0.1788 0.061 -0.0413 0.3496 8.396 -16.956 -16.71 6 1.3536 -0.3496 0.2889 2.1507 0.1741 1.186 0.0363 -0.014 -0.3445 0.1159 0.0876 -0.3426 0.0417 0.1464 -0.1239 0.0633 0.0277 -0.1313 0.0626 -0.0697 0.3585 12.201 -13.183 -19.435 7 1.9083 1.256 1.4568 2.9222 1.5771 2.5784 -0.0969 0.3942 -0.0155 -0.218 0.1006 -0.4128 -0.1543 0.3578 -0.0037 0.0959 -0.0158 -0.0498 0.141 -0.0079 0.2291 11.138 13.412 -32.875 8 0.7841 -0.6388 -0.2087 2.8866 -0.4064 1.9978 -0.009 0.1916 -0.0101 -0.0524 -0.0817 -0.5176 0.0377 0.4257 0.0907 0.0585 -0.0158 -0.0547 0.1912 -0.0202 0.3042 17.879 7.532 -29.377 9 2.138 -0.3554 -0.9461 0.7678 -0.0002 4.8625 -0.1186 0.2126 0.2776 -0.0709 0.0348 -0.2206 -0.4148 0.2602 0.0838 0.1697 -0.0841 -0.0915 0.0751 0.0131 0.2317 9.188 25.959 -27.807 10 2.8073 0.6691 -1.8256 1.8336 -0.378 3.8985 -0.1634 0.0988 -0.2173 -0.1137 0.1626 0.0768 0.1671 0.0337 0.0008 0.0883 0.0162 -0.1303 0.0458 -0.0272 0.3018 -7.103 -11.191 -23.933 11 0.8456 -0.4295 0.22 2.4769 -0.8822 1.1864 0.1231 0.0952 -0.295 -0.2161 0.0045 0.2203 0.1407 -0.0456 -0.1276 0.0906 -0.0153 -0.1461 0.0814 -0.0406 0.3037 -11.591 -12.289 -25.481 12 2.4544 0.2555 0.6531 4.1359 3.1806 3.4558 0.0345 -0.0253 -0.5546 0.277 0.0964 0.3629 0.1397 0.0564 -0.1309 0.161 -0.0458 -0.1184 0.0236 0.0838 0.4627 -10.86 -20.171 -12.881 13 1.8283 -1.48 1.2047 5.2078 -2.4326 1.8899 -0.0651 -0.2291 -0.1543 0.4998 0.1891 0.2375 -0.047 -0.2095 -0.124 0.1469 0.0283 -0.0341 0.1003 -0.0161 0.1122 -11.119 9.734 -3.542 14 2.6169 -1.1426 1.0427 3.2377 -1.3328 2.7056 -0.018 -0.5121 -0.3787 0.5147 0.2971 0.5596 0.025 -0.486 -0.2791 0.2114 0.0444 0.0048 0.1905 0.0188 0.2195 -14.332 9.258 0.958 15 1.2 0.1205 0.3993 2.1179 0.0359 1.2102 -0.0083 -0.2828 -0.0026 0.3225 0.0351 0.289 -0.0287 -0.2774 -0.0268 0.1296 0.0644 -0.0191 0.1303 -0.0323 0.1371 -15.209 12.158 -5.132 16 1.0329 -0.5908 0.8564 4.8749 -1.3521 2.235 0.021 0.0414 0.1039 0.2657 -0.0218 -0.1811 -0.0281 0.0993 0.0008 0.1404 0.0263 -0.1179 0.087 -0.0613 0.1587 4.744 13.308 -3.163 17 2.6171 2.2387 0.3609 2.7408 1.2205 1.0659 0.3062 -0.129 0.3922 0.2747 -0.1742 0.2043 0.0622 -0.0391 -0.132 0.3559 0.0175 -0.0987 0.0985 -0.0084 0.2146 5.593 15.254 4.646 18 1.313 0.4517 -0.0535 1.4039 -0.0146 0.6079 0.0411 -0.2272 0.0353 0.3356 0.0299 -0.2117 -0.0444 0.1241 -0.071 0.2221 0.0242 -0.184 0.1059 -0.0383 0.1829 9.672 9.932 0.615
精密化 TLSグループ 大きな表を表示 (5 x 18) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A3 - 39 2 X-RAY DIFFRACTION 2 A40 - 73 3 X-RAY DIFFRACTION 3 A74 - 151 4 X-RAY DIFFRACTION 4 B2 - 22 5 X-RAY DIFFRACTION 5 B23 - 87 6 X-RAY DIFFRACTION 6 B88 - 152 7 X-RAY DIFFRACTION 7 C3 - 87 8 X-RAY DIFFRACTION 8 C88 - 128 9 X-RAY DIFFRACTION 9 C129 - 153 10 X-RAY DIFFRACTION 10 D3 - 26 11 X-RAY DIFFRACTION 11 D27 - 125 12 X-RAY DIFFRACTION 12 D126 - 152 13 X-RAY DIFFRACTION 13 E0 - 25 14 X-RAY DIFFRACTION 14 E26 - 87 15 X-RAY DIFFRACTION 15 E88 - 153 16 X-RAY DIFFRACTION 16 F3 - 25 17 X-RAY DIFFRACTION 17 F26 - 53 18 X-RAY DIFFRACTION 18 F54 - 151