ソフトウェア 名称 バージョン 分類 PHENIX1.9_1692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 : フーリエ合成開始モデル : 4YKI解像度 : 1.34→38.988 Å / SU ML : 0.11 / 交差検証法 : THROUGHOUT / σ(F) : 1.38 / 位相誤差 : 15.76 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Selection details Rfree 0.1667 6166 5.06 % Random selection Rwork 0.1432 - - - obs 0.1444 121955 97.77 % -
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL精密化ステップ サイクル : LAST / 解像度 : 1.34→38.988 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4002 0 16 780 4798
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.009 4226 X-RAY DIFFRACTION f_angle_d1.239 5716 X-RAY DIFFRACTION f_dihedral_angle_d12.878 1556 X-RAY DIFFRACTION f_chiral_restr0.068 609 X-RAY DIFFRACTION f_plane_restr0.006 748
LS精密化 シェル 大きな表を表示 (7 x 30) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.3393-1.3545 0.2313 149 0.2183 2710 X-RAY DIFFRACTION 69 1.3545-1.3705 0.2556 182 0.2153 3134 X-RAY DIFFRACTION 80 1.3705-1.3872 0.2299 185 0.2159 3508 X-RAY DIFFRACTION 89 1.3872-1.4047 0.2385 190 0.2017 3784 X-RAY DIFFRACTION 96 1.4047-1.4232 0.2037 219 0.1771 3902 X-RAY DIFFRACTION 100 1.4232-1.4427 0.1758 199 0.1764 3965 X-RAY DIFFRACTION 100 1.4427-1.4633 0.1818 206 0.1671 3961 X-RAY DIFFRACTION 100 1.4633-1.4852 0.1868 210 0.1596 3912 X-RAY DIFFRACTION 100 1.4852-1.5084 0.1842 212 0.1571 3909 X-RAY DIFFRACTION 100 1.5084-1.5331 0.181 205 0.1522 3964 X-RAY DIFFRACTION 100 1.5331-1.5595 0.1861 214 0.1493 3952 X-RAY DIFFRACTION 100 1.5595-1.5879 0.1844 218 0.1496 3930 X-RAY DIFFRACTION 100 1.5879-1.6184 0.1717 199 0.1438 3940 X-RAY DIFFRACTION 100 1.6184-1.6515 0.192 216 0.1438 3946 X-RAY DIFFRACTION 100 1.6515-1.6874 0.1802 209 0.147 3953 X-RAY DIFFRACTION 100 1.6874-1.7266 0.1646 207 0.1447 3914 X-RAY DIFFRACTION 100 1.7266-1.7698 0.1712 209 0.1422 3990 X-RAY DIFFRACTION 100 1.7698-1.8177 0.1535 216 0.1371 3927 X-RAY DIFFRACTION 100 1.8177-1.8712 0.1581 203 0.143 3940 X-RAY DIFFRACTION 100 1.8712-1.9316 0.1599 217 0.1445 3956 X-RAY DIFFRACTION 100 1.9316-2.0006 0.169 207 0.142 3919 X-RAY DIFFRACTION 100 2.0006-2.0807 0.1515 202 0.1355 4002 X-RAY DIFFRACTION 100 2.0807-2.1754 0.1566 201 0.1338 3957 X-RAY DIFFRACTION 100 2.1754-2.29 0.1539 204 0.1336 3943 X-RAY DIFFRACTION 100 2.29-2.4335 0.163 195 0.1362 3953 X-RAY DIFFRACTION 100 2.4335-2.6214 0.1837 190 0.141 3972 X-RAY DIFFRACTION 100 2.6214-2.8851 0.1528 222 0.1437 3962 X-RAY DIFFRACTION 100 2.8851-3.3024 0.1541 202 0.1407 3966 X-RAY DIFFRACTION 100 3.3024-4.1599 0.1565 220 0.1232 3980 X-RAY DIFFRACTION 100 4.1599-39.0048 0.1597 258 0.1403 3938 X-RAY DIFFRACTION 100
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 10) 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 0.301 -0.0469 0.0187 0.0985 0.0001 0.1635 0.0071 -0.0215 -0.0659 -0.0309 -0.0309 -0.0168 0.0567 0.078 0.0002 0.1148 0.0182 -0.0032 0.0884 0.0055 0.1439 21.49 54.4283 49.7984 2 0.0788 -0.1437 0.1264 0.3285 -0.0789 0.4247 -0.0009 -0.0436 -0.0406 0.0149 -0.0056 0.0318 0.068 -0.0151 -0 0.103 -0.0013 -0.0159 0.0838 -0.0027 0.1673 12.5411 57.4647 54.4017 3 0.7456 -0.0364 -0.0891 0.2002 0.0974 0.3107 -0.0232 0.0933 -0.0083 -0.0491 -0.0057 0.013 -0.0087 -0.0563 0.0018 0.1058 -0.0137 -0.0083 0.0918 -0.0075 0.1301 3.6548 61.5562 42.7634 4 0.8387 0.2004 0.174 0.1426 -0.123 0.5434 -0.0927 0.1954 -0.0006 -0.0539 0.0429 0.0555 0.0314 0.0392 -0.009 0.0981 -0.0056 -0.0085 0.105 -0.0269 0.139 2.6076 59.6191 36.8872 5 0.2794 -0.0331 -0.0216 0.1001 -0.089 0.0816 -0.0183 0.0466 0.0341 -0.02 -0.018 -0.0433 -0.0181 -0.0286 -0 0.1094 -0.0098 -0.0018 0.1012 0.0053 0.1279 23.0286 68.8714 47.1636 6 0.6472 -0.0153 0.0497 0.2282 0.2696 0.3554 0.0258 0.0056 -0.0128 0.0215 -0.0148 0.02 -0.048 -0.083 0.0048 0.0942 0.0138 0.0044 0.0764 0.0039 0.0685 5.6656 94.8085 49.3467 7 0.2231 -0.2059 -0.1158 0.4029 0.2306 0.5869 0.0161 -0.0832 0.0145 0.0095 0.0066 -0.0229 -0.0319 0.0313 0.0067 0.0706 -0.0049 0.0015 0.0711 0.0004 0.0648 15.6616 93.1849 54.0833 8 0.6905 0.097 -0.5989 -0.0241 -0.1546 1.012 -0.0165 0.0825 -0.0784 -0.0169 -0.0031 -0.0244 0.0029 -0.0174 0.0229 0.0807 -0.0034 0.0053 0.0785 -0.0056 0.0629 25.1187 88.3308 36.0162 9 0.2021 -0.075 -0.0788 0.0102 0.0469 0.0486 -0.0485 0.0091 -0.0368 -0.0017 -0.0391 -0.0023 0.0149 -0.0032 -0 0.1032 -0.0042 0.0014 0.1043 -0.0128 0.1292 4.3155 79.4123 50.371 10 0.1017 -0.1976 -0.1248 0.3245 0.2172 0.1627 -0.1725 0.5739 -0.0275 -0.0054 -0.0425 -0.0333 0.0159 0.2523 -0.0281 0.116 -0.0268 -0.0194 0.3136 0.011 0.1067 5.6798 89.2804 29.0969
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 (chain A and resid 5:43)2 X-RAY DIFFRACTION 2 (chain A and resid 44:72)3 X-RAY DIFFRACTION 3 (chain A and resid 73:143)4 X-RAY DIFFRACTION 4 (chain A and resid 144:220)5 X-RAY DIFFRACTION 5 (chain A and resid 221:251)6 X-RAY DIFFRACTION 6 (chain B and resid 1:43)7 X-RAY DIFFRACTION 7 (chain B and resid 44:89)8 X-RAY DIFFRACTION 8 (chain B and resid 90:220)9 X-RAY DIFFRACTION 9 (chain B and resid 221:244)10 X-RAY DIFFRACTION 10 (chain B and resid 245:255)