ソフトウェア 名称 バージョン 分類 REFMAC5.8.0258精密化 PDB_EXTRACT3.25 データ抽出 HKL-3000データ削減 HKL-3000データスケーリング PHENIX位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 3.1→29.4 Å / Cor.coef. Fo :Fc : 0.939 / Cor.coef. Fo :Fc free : 0.923 / SU B : 52.217 / SU ML : 0.42 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R Free : 0.531 詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.2897 1307 4.9 % RANDOM Rwork 0.2337 - - - obs 0.2364 25380 99.77 % -
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原子変位パラメータ Biso max : 182.38 Å2 / Biso mean : 72.399 Å2 / Biso min : 22.39 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.58 Å2 0 Å2 0 Å2 2- - -2.27 Å2 0 Å2 3- - - -0.32 Å2
精密化ステップ サイクル : final / 解像度 : 3.1→29.4 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8456 0 0 88 8544 Biso mean - - - 46.4 - 残基数 - - - - 1080
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.004 0.013 8613 X-RAY DIFFRACTION r_bond_other_d0.001 0.018 7934 X-RAY DIFFRACTION r_angle_refined_deg1.241 1.66 11606 X-RAY DIFFRACTION r_angle_other_deg0.327 1.586 18629 X-RAY DIFFRACTION r_dihedral_angle_1_deg1.425 5 1082 X-RAY DIFFRACTION r_dihedral_angle_2_deg21.586 26.306 379 X-RAY DIFFRACTION r_dihedral_angle_3_deg7.371 15 1591 X-RAY DIFFRACTION r_dihedral_angle_4_deg13.201 15 8 X-RAY DIFFRACTION r_chiral_restr0.053 0.2 1217 X-RAY DIFFRACTION r_gen_planes_refined0.054 0.02 9462 X-RAY DIFFRACTION r_gen_planes_other0.052 0.02 1582
Refine LS restraints NCS Refine-ID : X-RAY DIFFRACTION / タイプ : interatomic distance / Weight position : 0.05
Ens-ID Dom-ID Auth asym-ID 数 Rms dev position (Å)1 1 A8150 0.1 1 2 B8150 0.1 2 1 A8047 0.11 2 2 C8047 0.11 3 1 A8152 0.1 3 2 D8152 0.1 4 1 B8131 0.1 4 2 C8131 0.1 5 1 B8132 0.1 5 2 D8132 0.1 6 1 C8148 0.1 6 2 D8148 0.1
LS精密化 シェル 解像度 : 3.1→3.18 Å / Rfactor Rfree error : 0 / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.39 102 - Rwork 0.35 1842 - all - 1944 - obs - - 99.95 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 20) 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 2.5332 -0.5461 -1.5688 1.9857 0.6153 2.7725 0.2055 0.0841 0.3445 -0.0963 0.1175 0.0024 -0.107 0.0784 -0.323 0.1141 0.0143 -0.0546 0.1812 0.075 0.206 19.4461 81.122 71.8553 2 2.1975 0.7217 -0.4411 2.4219 -0.3856 0.1251 -0.0121 0.1442 0.2411 0.0531 0.0928 0.0893 0.0112 -0.0147 -0.0807 0.1175 0.0277 -0.0178 0.2571 -0.0295 0.1099 10.3795 59.4765 87.2214 3 3.2881 -3.4828 -1.288 7.004 -1.1949 2.5153 0.0461 0.0125 -0.0152 -0.3182 -0.0953 0.0238 0.1782 0.0689 0.0492 0.0382 -0.0453 -0.0239 0.2055 0.0243 0.147 -1.3189 38.9194 94.8397 4 5.171 3.7297 -3.8593 3.2173 -1.7007 5.2644 -0.1731 0.1851 -0.1404 -0.1514 -0.0284 0 0.1394 -0.3885 0.2015 0.0797 0.0955 0.0356 0.2181 0.1067 0.3776 -3.4166 64.9468 87.3415 5 3.4894 1.2604 -2.1832 1.681 -0.485 7.2317 -0.1061 0.0155 -0.0128 -0.3121 0.0965 0.208 -0.0355 -0.6601 0.0096 0.1073 0.0639 -0.0624 0.3444 0.1245 0.2065 8.6046 79.6137 66.3715 6 2.9116 -3.3544 3.0264 5.0848 -1.4283 6.7569 0.4647 -0.1873 -0.3331 -0.2994 0.2378 0.1451 1.0033 -0.0978 -0.7025 0.2643 -0.0017 0.0163 0.1194 0.0024 0.259 24.0008 29.8107 67.8343 7 1.6538 0.4108 2.2436 0.2614 0.0642 4.64 0.0206 0.1974 -0.1436 0.0534 0.146 -0.0721 -0.0588 0.0475 -0.1666 0.2651 0.0157 -0.0264 0.2171 -0.1237 0.2318 20.3857 40.0358 73.3874 8 2.0804 0.6536 0.6115 1.7706 0.7155 0.3591 0.1243 0.1465 -0.1065 0.0227 -0.0607 -0.0633 0.0268 0.0209 -0.0635 0.1068 0.0123 0.0054 0.2558 0.006 0.1319 31.3558 64.0035 88.6314 9 4.4929 -0.8336 1.8621 5.8089 -0.0828 0.7856 -0.0202 0.1264 -0.0605 -0.3751 0.0474 0.1336 -0.0256 0.0755 -0.0272 0.0256 -0.0051 -0.0009 0.2991 0.0367 0.2251 42.1492 79.3714 92.7247 10 1.9857 2.1712 1.7816 2.5081 2.3291 3.5119 -0.2708 0.316 -0.226 -0.303 0.3215 -0.3121 -0.1824 0.4247 -0.0506 0.1126 0.0775 -0.0233 0.2767 -0.1091 0.3571 38.8743 48.2128 78.1133 11 9.6895 -0.6222 -1.2355 1.663 -1.0889 1.0103 0.0227 0.8356 0.0788 0.1285 -0.0216 -0.1 -0.1205 -0.1184 -0.0011 0.1564 -0.0603 0.0545 0.2323 -0.0737 0.2832 32.478 78.819 57.3721 12 1.8431 0.7015 1.0509 0.8884 0.815 1.1517 0.1273 -0.0276 0.2953 -0.0802 0.117 -0.2267 0.0835 -0.2815 -0.2443 0.209 -0.1449 0.0886 0.5806 0.0638 0.4655 28.498 66.4726 44.6934 13 1.6251 0.1666 -0.603 1.8278 -0.0204 0.3547 0.0982 -0.1962 -0.2192 0.0052 0.0437 -0.009 -0.0029 0.0184 -0.1419 0.0735 0.0348 -0.0791 0.2377 0.0693 0.4109 29.3973 32.7796 30.48 14 0.6143 -1.9284 -0.5527 6.1346 1.7791 0.5223 -0.1102 -0.0324 -0.0381 0.4082 -0.0093 0.2801 0.1357 -0.0402 0.1195 0.0795 -0.1023 0.0863 0.2106 -0.1899 0.3473 42.211 52.166 40.1582 15 5.636 -0.6203 1.7582 0.1315 -0.422 4.5668 -0.298 -0.8367 -0.2849 0.0067 0.0889 -0.1579 0.4422 0.6272 0.2091 0.2065 0.1274 0.0212 0.3702 -0.0333 0.6314 42.2695 69.4949 59.797 16 5.6302 -1.1241 4.2457 1.6194 -0.791 3.2047 0.107 0.5473 -0.3426 -0.2946 0.1383 0.4851 0.056 0.4309 -0.2453 0.2761 -0.1585 0.0186 0.2577 0.0388 0.231 6.7137 39.7011 53.9834 17 3.2125 -1.7195 -1.9704 1.6141 -0.0407 2.9611 0.0503 0.2264 -0.0185 -0.2249 -0.2341 -0.1369 0.3391 0.0035 0.1838 0.2562 -0.1868 -0.104 0.5436 0.0893 0.1707 20.1793 50.3344 40.3985 18 1.3259 -0.5094 0.2058 0.9598 -0.2328 0.4221 0.1048 -0.5637 0.1983 -0.3084 0.0947 0.1759 0.228 -0.0458 -0.1994 0.2275 -0.022 -0.1032 0.358 -0.0538 0.3163 7.3027 67.7622 36.6855 19 2.8343 1.8342 1.4416 2.0664 0.457 3.6594 0.2453 -0.1396 0.29 0.0728 -0.1064 -0.2021 0.0368 0.0569 -0.1388 0.1268 0.0249 0.0646 0.1789 0.0087 0.3303 14.4173 84.0909 29.0812 20 2.4377 -1.823 0.9268 4.7497 -4.1509 3.8867 -0.2695 -0.2531 0.1369 0.3619 0.4901 0.1723 -0.25 -0.4254 -0.2206 0.2809 -0.1601 -0.0878 0.2362 0.0786 0.2588 -2.2304 56.0983 46.9106
精密化 TLSグループ 大きな表を表示 (5 x 20) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A31 - 82 2 X-RAY DIFFRACTION 2 A83 - 174 3 X-RAY DIFFRACTION 3 A175 - 243 4 X-RAY DIFFRACTION 4 A244 - 277 5 X-RAY DIFFRACTION 5 A278 - 301 6 X-RAY DIFFRACTION 6 B31 - 44 7 X-RAY DIFFRACTION 7 B45 - 82 8 X-RAY DIFFRACTION 8 B83 - 184 9 X-RAY DIFFRACTION 9 B185 - 244 10 X-RAY DIFFRACTION 10 B245 - 300 11 X-RAY DIFFRACTION 11 C32 - 58 12 X-RAY DIFFRACTION 12 C59 - 134 13 X-RAY DIFFRACTION 13 C135 - 249 14 X-RAY DIFFRACTION 14 C250 - 277 15 X-RAY DIFFRACTION 15 C278 - 300 16 X-RAY DIFFRACTION 16 D32 - 79 17 X-RAY DIFFRACTION 17 D80 - 112 18 X-RAY DIFFRACTION 18 D113 - 173 19 X-RAY DIFFRACTION 19 D174 - 246 20 X-RAY DIFFRACTION 20 D247 - 301