ソフトウェア 名称 バージョン 分類 NB REFMAC5.5.0109精密化 Show PDB_EXTRACT3.1 データ抽出 Show SBC-Collectデータ収集 HKL-3000データ削減 HKL-3000データスケーリング HKL-3000位相決定 MLPHARE位相決定 直接法位相決定 SHELXDE位相決定 RESOLVE位相決定 ARP/wARPモデル構築 Cootモデル構築
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.3→50 Å / Cor.coef. Fo :Fc : 0.957 / Cor.coef. Fo :Fc free : 0.944 / Occupancy max : 1 / Occupancy min : 0.5 / SU B : 10.381 / SU ML : 0.114 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R Free : 0.164 立体化学のターゲット値 : MAXIMUM LIKELIHOOD WITH PHASES詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.2178 2585 5.1 % RANDOM Rwork 0.1812 - - - all 0.183 50884 - - obs 0.183 50884 99.46 % -
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 : 1.4 Å / 溶媒モデル : MASK原子変位パラメータ Biso max : 129.48 Å2 / Biso mean : 49.4493 Å2 / Biso min : 26.95 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.07 Å2 0 Å2 0 Å2 2- - -0.07 Å2 0 Å2 3- - - 0.14 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 4728 0 0 186 4914
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.013 0.021 4891 X-RAY DIFFRACTION r_angle_refined_deg1.362 1.964 6654 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.153 5 636 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.092 22.684 231 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.886 15 776 X-RAY DIFFRACTION r_dihedral_angle_4_deg19.365 15 60 X-RAY DIFFRACTION r_chiral_restr0.087 0.2 746 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.021 3824 X-RAY DIFFRACTION r_mcbond_it1.593 1.5 3157 X-RAY DIFFRACTION r_mcangle_it2.958 2 5029 X-RAY DIFFRACTION r_scbond_it3.337 3 1734 X-RAY DIFFRACTION r_scangle_it5.76 4.5 1625 X-RAY DIFFRACTION r_rigid_bond_restr1.675 3 4891
LS精密化 シェル 解像度 : 2.302→2.361 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.271 189 - Rwork 0.216 3557 - all - 3746 - obs - 3746 99.02 %
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 0.2992 0.0478 -0.2141 0.2243 0.0303 0.2846 0.0031 0.0279 -0.0037 -0.0117 -0.003 0.0139 -0.0027 -0.0349 -0.0001 0.1193 -0.0004 0.0046 0.1259 0.0031 0.13 62.8673 43.066 25.1937 2 2.476 -4.0817 -0.651 18.2131 6.5486 7.9254 0.1306 0.5914 0.4568 -0.3303 -0.5644 0.3355 -0.1976 -0.1884 0.4337 0.0627 -0.0486 0.0487 0.2914 0.0539 0.3518 49.0645 33.2979 51.6575 3 0.1012 0.0675 0.104 0.0596 -0.0281 0.7856 0.0078 -0.0024 -0.0131 -0.0031 -0.0018 -0.0127 0.0515 -0.0629 -0.006 0.1201 -0.0063 0.0035 0.1313 0.003 0.1416 56.1647 33.1176 41.6572 4 0.0072 0.0077 0.0024 0.3047 -0.0327 0.0073 -0.0359 -0.0162 0.009 0.0586 0.0641 0.0603 -0.0303 -0.0059 -0.0282 0.1682 -0.0034 0.0306 0.1581 0.0138 0.1735 52.0146 44.6699 56.9041 5 0.0194 -0.0131 0.0415 0.1916 -0.0366 0.1218 0.0056 -0.0128 -0.0195 0.0301 0.0235 -0.0228 0.016 0.032 -0.0291 0.1278 -0.0073 0.0069 0.1268 0.0062 0.1391 59.7946 36.7865 49.2319 6 2.9135 -2.282 1.8757 5.3629 -3.3328 2.179 -0.0205 -0.1836 0.0817 0.1756 0.0305 0.0448 -0.0975 -0.0638 -0.01 0.1393 0.0139 0.0156 0.1346 -0.006 0.1339 58.0309 61.8278 52.3884 7 0.0754 0.0241 0.006 0.0344 -0.1028 0.4224 0.0143 -0.021 -0.0038 0.0125 -0.0046 -0.0062 -0.0112 0.0007 -0.0097 0.1242 -0.0016 0.0081 0.1255 0.0025 0.1413 69.2757 47.2309 52.2681 8 4.468 -1.8133 -2.7407 0.7369 1.1121 1.6835 0.1045 0.4348 0.075 -0.021 -0.1181 -0.0404 -0.0242 -0.2829 0.0136 0.1265 -0.0277 0.0241 0.1572 0.0189 0.1081 62.4626 61.5248 40.9754 9 0.1627 -0.0848 0.0217 0.0766 -0.0434 0.1034 0.0055 -0.0036 -0.0112 0.0003 0.0055 -0.0009 -0.0328 0.0169 -0.011 0.1221 -0.0062 0.0071 0.1248 0.0029 0.1364 73.2628 52.4497 34.0364 10 0.847 0.0023 -0.0316 1.0684 0.0205 0.0016 0.0323 -0.0369 -0.1033 -0.047 -0.0235 -0.0563 -0.003 0.001 -0.0088 0.0092 0.0109 0.0191 0.1415 -0.0057 0.1405 69.1632 32.287 32.8285 11 0.2524 -0.0183 -0.1168 0.2409 0.0349 0.2897 0.0009 -0.0239 0.0003 0.0002 0.003 -0.0204 0.0184 0.0341 -0.0039 0.1177 0.0033 0.0054 0.1243 -0.0037 0.1314 83.7277 43.1453 11.4667 12 5.4946 -3.0466 -1.0926 15.4662 -6.5848 3.9706 -0.0882 -0.5093 0.5219 0.5055 -0.0619 -0.8488 -0.2382 0.261 0.15 0.0668 0.0435 -0.0074 0.1875 0.0092 0.204 97.7276 33.4188 -14.7119 13 0.0944 0.072 -0.0628 0.0759 -0.0342 0.0557 0.0006 -0.0173 -0.0053 0.0054 0.015 -0.0139 0.0239 0.0364 -0.0156 0.1278 0.0156 0.0038 0.1337 -0.007 0.143 90.6953 33.0403 -4.8311 14 0.0889 -0.244 -0.0042 1.9705 0.4231 0.1383 -0.0016 0.0223 0.0617 -0.2336 0.0465 -0.256 -0.1027 0.0272 -0.0449 0.1313 0.0014 0.0317 0.1369 -0.0075 0.1917 94.7689 44.5691 -20.0859 15 0.0772 0.1609 -0.0388 0.3446 -0.0841 0.0207 -0.0064 0.0129 -0.0054 -0.0362 0.013 0.0124 0.0098 -0.0014 -0.0067 0.1338 0.0154 0.0045 0.1305 -0.0045 0.1344 87.0124 36.7251 -12.3842 16 1.0759 1.7685 1.4318 3.018 2.4549 1.9981 0.0124 0.0906 -0.1357 -0.0129 0.0734 -0.1378 -0.0146 0.0395 -0.0858 0.1304 0.0001 0.0088 0.1472 -0.0168 0.1502 89.1255 61.9086 -15.4025 17 0.1917 -0.0405 -0.0467 0.0345 0.0878 0.2537 0.0123 0.0199 0.0081 -0.0112 -0.0045 0.0063 -0.0124 -0.005 -0.0078 0.1278 0.002 0.0052 0.1272 -0.0032 0.1391 77.6121 47.2466 -15.3513 18 7.2103 4.8083 -8.6013 3.6238 -6.2728 10.9522 0.4801 -0.8363 -0.1825 0.1634 -0.5817 0.0839 -0.3232 1.215 0.1016 0.1459 -0.0082 0.0079 0.1661 -0.0544 0.1521 84.5893 61.4395 -4.1935 19 0.1224 -0.0841 -0.0498 0.0599 0.0372 0.1412 -0.0013 0.0046 0.0029 -0.01 0.0077 0.0024 -0.0319 -0.0165 -0.0063 0.1253 0.0033 0.0057 0.1245 -0.0031 0.1369 73.528 52.4855 2.8486 20 1.9416 -1.1587 0.3047 1.9537 -0.575 0.1703 -0.038 -0.0774 -0.101 0.0754 0.0641 0.0826 -0.0223 -0.0173 -0.0261 0.0258 0.0316 0.0385 0.1372 -0.0082 0.1361 77.6969 32.3642 4.0892
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 A7 - 77 2 X-RAY DIFFRACTION 2 A78 - 104 3 X-RAY DIFFRACTION 3 A105 - 133 4 X-RAY DIFFRACTION 4 A134 - 152 5 X-RAY DIFFRACTION 5 A153 - 183 6 X-RAY DIFFRACTION 6 A184 - 193 7 X-RAY DIFFRACTION 7 A194 - 261 8 X-RAY DIFFRACTION 8 A262 - 272 9 X-RAY DIFFRACTION 9 A273 - 321 10 X-RAY DIFFRACTION 10 A322 - 332 11 X-RAY DIFFRACTION 11 B7 - 77 12 X-RAY DIFFRACTION 12 B78 - 104 13 X-RAY DIFFRACTION 13 B105 - 133 14 X-RAY DIFFRACTION 14 B134 - 152 15 X-RAY DIFFRACTION 15 B153 - 183 16 X-RAY DIFFRACTION 16 B184 - 193 17 X-RAY DIFFRACTION 17 B194 - 261 18 X-RAY DIFFRACTION 18 B262 - 272 19 X-RAY DIFFRACTION 19 B273 - 321 20 X-RAY DIFFRACTION 20 B322 - 332