ソフトウェア 名称 バージョン 分類 Blu-IceMaxデータ収集 CRANK位相決定 SHELXCD位相決定 SHELXEモデル構築 bp3モデル構築 SOLOMON位相決定 ARP/wARPモデル構築 BUCCANEERモデル構築 REFMAC5.5.0102精密化 HKL-2000データ削減 HKL-2000データスケーリング bp3位相決定 BUCCANEER位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.01→30 Å / Cor.coef. Fo :Fc : 0.971 / Cor.coef. Fo :Fc free : 0.957 / SU B : 6.969 / SU ML : 0.094 / TLS residual ADP flag : LIKELY RESIDUAL / Isotropic thermal model : isotropic / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.173 / ESU R Free : 0.147 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.19754 1998 5 % RANDOM Rwork 0.16091 - - - all 0.16279 37836 - - obs 0.16279 37836 99.28 % -
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 mean : 20.402 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.45 Å2 0 Å2 -0.17 Å2 2- - -0.39 Å2 -0 Å2 3- - - -1.12 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.01→30 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4482 0 29 285 4796
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_d0.011 0.022 4798 X-RAY DIFFRACTION r_bond_other_d0 0.02 3081 X-RAY DIFFRACTION r_angle_refined_deg1.472 1.928 6546 X-RAY DIFFRACTION r_angle_other_deg0.845 3 7618 X-RAY DIFFRACTION r_dihedral_angle_1_deg3.877 5 606 X-RAY DIFFRACTION r_dihedral_angle_2_deg36.28 25.801 231 X-RAY DIFFRACTION r_dihedral_angle_3_deg10.323 15 802 X-RAY DIFFRACTION r_dihedral_angle_4_deg10.177 15 5 X-RAY DIFFRACTION r_chiral_restr0.096 0.2 728 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 5459 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 922 X-RAY DIFFRACTION r_mcbond_it0.868 1.5 2958 X-RAY DIFFRACTION r_mcbond_other0.277 1.5 1188 X-RAY DIFFRACTION r_mcangle_it1.563 2 4828 X-RAY DIFFRACTION r_scbond_it2.616 3 1840 X-RAY DIFFRACTION r_scangle_it4.014 4.5 1718
LS精密化 シェル 解像度 : 2.01→2.06 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.226 137 - Rwork 0.193 2563 - obs - 2563 92.91 %
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 3.3907 -0.1931 0.6196 1.6218 0.0769 2.0684 0.0985 -0.3437 -0.2432 0.2047 0.0229 -0.1261 0.052 -0.0577 -0.1214 0.0594 -0.0033 0.0037 0.0495 0.0503 0.0916 11.3324 -6.5499 47.2025 2 3.2084 0.4679 0.5991 0.9093 -0.1526 1.348 0.0277 0.049 -0.2359 0.0612 0.0173 -0.1677 0.0975 0.2092 -0.045 0.0512 0.0276 -0.0096 0.0467 0.0174 0.1297 19.2773 -2.9686 38.4622 3 2.4487 0.7483 0.6707 1.123 0.0698 1.8793 -0.0073 0.0311 0.0359 0.0346 0.0624 0.1255 -0.0986 -0.1449 -0.055 0.0153 0.0167 0.0131 0.0229 0.0234 0.0558 7.6832 2.8674 38.8242 4 6.3416 1.6551 -0.2833 3.1794 0.0509 0.9021 -0.1313 0.1617 0.8235 -0.0525 0.1781 0.1452 -0.2282 0.0396 -0.0468 0.1593 -0.0017 -0.0158 0.0628 0.0351 0.1155 18.1078 20.1561 32.2061 5 2.6826 0.4775 0.1072 2.3099 0.4916 2.9935 -0.1538 0.5135 0.112 -0.4572 0.1746 -0.076 -0.2378 0.134 -0.0208 0.1613 -0.047 0.0175 0.1181 0.046 0.0681 20.6414 13.2402 22.3021 6 3.277 0.864 0.9539 1.627 0.1867 2.382 -0.0151 0.314 -0.1838 -0.1973 0.0748 -0.1447 -0.0033 0.0826 -0.0596 0.0321 -0.0001 0.0189 0.0308 -0.0145 0.0291 20.1746 2.9606 28.2951 7 2.9066 0.6744 0.4105 1.9048 0.1178 2.3846 -0.0044 -0.0163 0.2477 -0.0196 -0.0079 0.1518 -0.2243 -0.1054 0.0123 0.0808 0.0214 0.0057 0.0172 0.0228 0.0759 13.2963 13.588 34.4155 8 4.6407 0.1427 -2.3076 1.5002 1.1166 4.7913 0.03 0.0366 -0.1439 0.0308 -0.1193 0.146 0.1357 -0.416 0.0892 0.0737 0.0014 -0.0416 0.1301 0.0519 0.0965 -1.1268 -6.2353 42.5692 9 5.3434 0.4456 0.7964 6.2816 -1.1489 3.7962 0.039 -0.7752 -0.3458 0.7105 -0.1822 0.2891 -0.2613 -0.275 0.1432 0.4046 -0.0096 0.0348 0.399 0.1198 0.1074 0.2013 -19.2612 95.4525 10 3.2849 0.6438 0.2268 3.1791 -0.5739 3.6765 0.0173 -0.3449 -0.0525 0.4779 -0.1557 0.0315 -0.1296 0.0744 0.1383 0.1927 -0.0286 -0.0012 0.2381 0.1254 0.078 3.7371 -16.3488 84.4522 11 11.6011 13.5286 7.7036 16.9606 10.2628 6.5802 0.0487 0.1119 -1.3223 0.5768 0.6329 -1.3069 0.6222 0.9032 -0.6816 0.5136 0.1571 -0.0872 1.0325 0.2683 0.635 18.5264 -21.6395 78.7253 12 6.3374 -1.5057 -0.5097 2.6198 0.2751 7.7011 -0.0682 0.3921 -0.3061 -0.2055 -0.0222 -0.0115 0.2416 -0.3263 0.0904 0.1496 -0.0968 0.0037 0.1149 0.0588 0.2266 -1.8493 -18.4284 58.6865 13 1.7599 0.6606 -0.34 2.4211 -0.4802 3.0474 0.0006 -0.0475 0.0934 0.1684 -0.0085 0.0536 -0.3082 0.0035 0.0079 0.1177 -0.0214 -0.0191 0.105 0.0571 0.1036 1.9428 -7.074 68.2614 14 3.7899 2.0968 -0.0203 3.8712 -0.7121 3.8794 -0.0578 -0.1873 -0.3245 -0.0505 -0.0693 -0.1828 0.2391 0.1481 0.1271 0.0921 0.0011 -0.0008 0.1045 0.0972 0.0976 4.9917 -17.946 70.5281 15 6.9355 0.5143 9.5121 0.7776 0.4064 24.5562 0.2258 -0.3729 -0.5251 0.2794 -0.2535 -0.2645 0.8668 0.8116 0.0277 0.3485 0.0245 -0.0158 0.3784 0.2879 0.4338 13.4358 -27.0559 84.968 16 18.6524 -10.7207 2.7866 32.6116 -11.5825 8.6256 -0.3181 -1.0194 0.6025 1.1233 0.0339 -0.5807 -0.7843 0.7734 0.2842 0.4624 -0.1915 -0.2133 0.5751 0.0743 0.1139 14.16 -11.5153 96.6708
精密化 TLSグループ 大きな表を表示 (5 x 16) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A2 - 43 2 X-RAY DIFFRACTION 2 A44 - 75 3 X-RAY DIFFRACTION 3 A76 - 111 4 X-RAY DIFFRACTION 4 A112 - 144 5 X-RAY DIFFRACTION 5 B3 - 46 6 X-RAY DIFFRACTION 6 B47 - 78 7 X-RAY DIFFRACTION 7 B79 - 119 8 X-RAY DIFFRACTION 8 B120 - 144 9 X-RAY DIFFRACTION 9 C4 - 36 10 X-RAY DIFFRACTION 10 C37 - 108 11 X-RAY DIFFRACTION 11 C109 - 119 12 X-RAY DIFFRACTION 12 C120 - 144 13 X-RAY DIFFRACTION 13 D2 - 78 14 X-RAY DIFFRACTION 14 D79 - 112 15 X-RAY DIFFRACTION 15 D113 - 130 16 X-RAY DIFFRACTION 16 D131 - 144