ソフトウェア 名称 バージョン 分類 Blu-IceMaxデータ収集 PHENIX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 PHENIX位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 2PD0解像度 : 2.35→29.4 Å / Cor.coef. Fo :Fc : 0.956 / Cor.coef. Fo :Fc free : 0.926 / SU B : 15.767 / SU ML : 0.171 Isotropic thermal model : Thermal Factors Individually Refined交差検証法 : THROUGHOUT / ESU R : 0.364 / ESU R Free : 0.257 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.25826 1026 5.1 % RANDOM Rwork 0.20232 - - - all 0.20509 19076 - - obs 0.20509 19076 99.96 % -
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 : 53.823 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.51 Å2 0 Å2 -0 Å2 2- - 1.53 Å2 0 Å2 3- - - -1.02 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.35→29.4 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3172 0 0 98 3270
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_d0.013 0.022 3294 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 2252 X-RAY DIFFRACTION r_angle_refined_deg1.471 1.977 4489 X-RAY DIFFRACTION r_angle_other_deg0.851 3 5489 X-RAY DIFFRACTION r_dihedral_angle_1_deg2.609 5 406 X-RAY DIFFRACTION r_dihedral_angle_2_deg22.658 23.724 145 X-RAY DIFFRACTION r_dihedral_angle_3_deg11.99 15 536 X-RAY DIFFRACTION r_dihedral_angle_4_deg10.074 15 22 X-RAY DIFFRACTION r_chiral_restr0.092 0.2 497 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.021 3654 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 662 X-RAY DIFFRACTION r_mcbond_it1.235 1.5 2051 X-RAY DIFFRACTION r_mcbond_other0.289 1.5 800 X-RAY DIFFRACTION r_mcangle_it2.223 2 3316 X-RAY DIFFRACTION r_scbond_it3.053 3 1243 X-RAY DIFFRACTION r_scangle_it4.433 4.5 1173
LS精密化 シェル 解像度 : 2.35→2.411 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.332 72 - Rwork 0.273 1382 - obs - 1382 99.86 %
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 2.6622 -0.3175 0.22 4.6581 2.8712 6.9739 -0.0408 -0.3317 0.5125 -0.0565 -0.0777 0.0428 -0.4628 -0.0704 0.1185 0.1966 0.0272 0.0404 0.1315 -0.0613 0.1783 15.8203 -6.5381 17.3904 2 4.0044 1.1729 -2.1083 1.4411 -0.4341 4.1069 0.0836 0.0334 0.4134 0.0124 0.0597 0.1728 -0.4079 0.0498 -0.1432 0.0629 -0.0061 -0.017 0.0147 0.01 0.0652 7.8287 -13.794 -8.7768 3 3.5274 0.4597 1.7938 3.4617 4.3519 5.9404 -0.0358 0.0102 0.2829 -0.6357 0.066 -0.1632 -0.8181 -0.0529 -0.0302 0.2408 0.0346 -0.0304 0.2643 -0.0824 0.136 14.7268 -10.0938 11.7619 4 6.1674 0.8659 -1.814 11.7822 -1.9438 3.8228 -0.3185 0.4774 0.3905 -2.5031 -0.0434 -0.0066 0.223 0.17 0.3619 1.0067 -0.1066 -0.0172 0.5115 -0.081 0.4768 21.5977 11.8281 13.4232 5 7.1964 8.9564 6.243 18.9358 16.3307 15.3463 -0.2684 0.0938 0.1741 -1.6547 0.1204 -0.0369 -1.6534 -0.0663 0.1481 0.3034 0.0497 0.0448 0.1124 -0.0661 0.1624 17.0124 -4.3546 13.4544 6 4.5409 -2.6501 3.3872 4.4024 2.6425 10.0724 -0.3834 -0.0613 0.2134 0.2667 0.1221 -0.142 -0.254 0.0798 0.2613 0.0687 -0.0262 -0.0414 0.1417 -0.0535 0.2301 20.2814 -15.3173 4.1486 7 6.0118 0.25 -0.8008 6.2628 -1.3567 5.4714 -0.1224 0.1604 1.0052 -0.1902 0.1722 -0.4193 -0.6645 0.6541 -0.0498 0.1187 -0.1043 -0.0094 0.2055 -0.0077 0.2548 25.4414 -9.9469 -8.4542 8 10.5692 -1.2115 1.7252 0.9909 1.9843 5.9406 0.0694 0.4561 0.9029 -0.3591 -0.1062 -0.1094 -0.844 -0.1248 0.0368 0.2246 -0.0043 0.0161 0.138 0.1125 0.2962 4.9473 -12.1709 -10.1253 9 10.3471 -0.6542 -1.4193 3.7623 2.2936 4.4235 -0.1617 1.0047 -0.1899 -0.4034 0.0338 -0.2067 -0.1707 0.1041 0.1279 0.4611 0.0049 -0.0515 0.4627 0.0404 0.2338 24.6942 -20.2531 -44.0085 10 4.2291 0.1478 0.9785 1.4843 0.371 4.0492 0.0201 0.4899 -0.1349 -0.1918 0.0869 -0.0548 0.144 0.2459 -0.107 0.0972 -0.0202 0.0141 0.1314 0.0305 0.0561 12.8025 -21.2338 -21.845 11 29.8779 0.6321 -5.9293 0.1032 -0.7385 5.507 -0.3162 0.1861 0.6475 -0.0057 0.0277 -0.0384 -0.1288 -0.3528 0.2885 0.3381 0.0464 -0.0657 0.3938 0.0376 0.1547 18.8436 -18.8806 -40.2573 12 12.7278 -0.5395 4.8163 5.2742 -0.8857 9.6903 -0.1884 0.792 0.1539 -0.3546 -0.0477 -0.0409 0.181 -0.1296 0.2361 0.2148 -0.0306 0.0201 0.3569 0.057 0.1292 41.5535 -18.5952 -37.2223 13 19.2806 1.3761 -1.8009 2.6654 0.1733 1.3383 0.1415 0.5666 0.1258 0.1019 -0.0767 -0.1497 -0.2673 -0.1944 -0.0648 0.2556 0.0149 -0.002 0.2859 0.0365 0.0469 25.4787 -18.7195 -40.6761 14 0.2019 -1.2783 0.3817 9.8165 -2.9017 29.5316 0.294 0.1156 0.0133 -1.1926 -0.0356 0.0218 -1.4839 0.5335 -0.2584 0.5284 0.0913 0.1024 0.5116 0.0379 0.5393 15.8924 -10.9845 -35.1489 15 12.8167 5.7081 4.8001 3.1766 3.6792 11.2013 0.0243 0.5622 0.0269 -0.2698 0.278 -0.479 -0.6966 1.1404 -0.3022 0.423 -0.1494 0.0656 0.3313 0.1546 0.5961 21.7636 -5.8098 -22.2622 16 2.1317 1.4922 -0.0854 5.7934 -2.2426 7.5652 0.0225 0.007 -0.3088 0.1826 -0.1399 -0.2276 0.4216 0.4308 0.1174 0.2728 -0.0285 0.0306 0.2771 0.023 0.2209 13.1473 -24.1136 -20.1851
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 A14 - 87 2 X-RAY DIFFRACTION 2 A88 - 128 3 X-RAY DIFFRACTION 3 A129 - 140 4 X-RAY DIFFRACTION 4 A141 - 161 5 X-RAY DIFFRACTION 5 A162 - 174 6 X-RAY DIFFRACTION 6 A175 - 182 7 X-RAY DIFFRACTION 7 A183 - 214 8 X-RAY DIFFRACTION 8 A215 - 227 9 X-RAY DIFFRACTION 9 B15 - 87 10 X-RAY DIFFRACTION 10 B88 - 128 11 X-RAY DIFFRACTION 11 B129 - 140 12 X-RAY DIFFRACTION 12 B141 - 161 13 X-RAY DIFFRACTION 13 B162 - 174 14 X-RAY DIFFRACTION 14 B175 - 182 15 X-RAY DIFFRACTION 15 B183 - 214 16 X-RAY DIFFRACTION 16 B215 - 227