ソフトウェア 名称 バージョン 分類 XSCALEデータスケーリング PHENIX1.8.4_1496精密化 PDB_EXTRACT3.15 データ抽出 XDSデータ削減 PHASER位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 5Y0R解像度 : 2.103→49.889 Å / SU ML : 0.24 / 交差検証法 : FREE R-VALUE / σ(F) : 1.36 / 位相誤差 : 21.74 Rfactor 反射数 %反射 Rfree 0.2074 6444 5 % Rwork 0.1688 - - obs 0.1707 128886 99.72 %
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å原子変位パラメータ Biso max : 180.51 Å2 / Biso mean : 44.19 Å2 / Biso min : 13.33 Å2 精密化ステップ サイクル : final / 解像度 : 2.103→49.889 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 13848 0 88 622 14558 Biso mean - - 52.75 39.67 - 残基数 - - - - 1692
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.008 14214 X-RAY DIFFRACTION f_angle_d1.055 19040 X-RAY DIFFRACTION f_chiral_restr0.045 2032 X-RAY DIFFRACTION f_plane_restr0.005 2452 X-RAY DIFFRACTION f_dihedral_angle_d14.101 5370
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 30
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 Num. reflection all % reflection obs (%)2.1032-2.1271 0.3136 202 0.2819 3842 4044 93 2.1271-2.1521 0.2816 213 0.2604 4057 4270 100 2.1521-2.1783 0.3042 214 0.2479 4065 4279 100 2.1783-2.2059 0.2791 213 0.2383 4046 4259 100 2.2059-2.2349 0.2786 215 0.2328 4083 4298 100 2.2349-2.2656 0.2845 215 0.2302 4079 4294 100 2.2656-2.2979 0.2766 213 0.213 4046 4259 100 2.2979-2.3322 0.2588 216 0.2134 4110 4326 100 2.3322-2.3687 0.2551 214 0.1947 4062 4276 100 2.3687-2.4075 0.2331 214 0.1923 4068 4282 100 2.4075-2.449 0.2514 216 0.1867 4096 4312 100 2.449-2.4935 0.244 215 0.1872 4089 4304 100 2.4935-2.5415 0.2347 214 0.1887 4063 4277 100 2.5415-2.5934 0.2299 215 0.1855 4081 4296 100 2.5934-2.6498 0.226 215 0.1805 4089 4304 100 2.6498-2.7114 0.2579 214 0.1798 4080 4294 100 2.7114-2.7792 0.2094 213 0.1719 4043 4256 100 2.7792-2.8543 0.2271 215 0.1689 4072 4287 100 2.8543-2.9383 0.2181 215 0.1794 4100 4315 100 2.9383-3.0331 0.2268 216 0.1806 4087 4303 100 3.0331-3.1415 0.2382 215 0.1781 4099 4314 100 3.1415-3.2673 0.2199 217 0.1819 4114 4331 100 3.2673-3.416 0.2096 215 0.1769 4080 4295 100 3.416-3.596 0.1933 214 0.1663 4077 4291 100 3.596-3.8212 0.1872 216 0.1568 4101 4317 100 3.8212-4.1162 0.1655 217 0.1382 4132 4349 100 4.1162-4.5301 0.1514 217 0.1242 4115 4332 100 4.5301-5.1851 0.1684 217 0.1249 4112 4329 100 5.1851-6.5303 0.1905 218 0.1544 4148 4366 100 6.5303-49.9026 0.1492 221 0.1405 4206 4427 100
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 1.3631 -0.1185 0.4026 1.235 0.0586 2.8839 -0.0342 -0.0018 0.1074 0.046 0.0116 -0.1156 -0.1523 0.2579 0.0316 0.1227 -0.0174 -0.0062 0.1917 -0.004 0.2251 55.7783 77.4176 126.3596 2 2.5323 -1.0505 0.4398 7.4948 -0.7609 2.409 0.0143 0.2091 0.6355 -0.153 -0.1007 -0.233 -0.4955 0.2315 0.0323 0.3037 -0.0634 -0.0132 0.2677 0.0169 0.3453 50.9162 99.1033 132.9193 3 5.8197 -0.4249 -3.9717 8.7232 4.1575 4.4517 -0.1514 -0.207 0.7225 -0.6311 0.2928 -0.3904 -1.0746 0.6297 -0.1518 0.7455 -0.1567 -0.0694 0.7007 0.0277 0.5026 69.9081 87.777 118.1946 4 0.4384 0.1446 0.1065 1.0764 -0.1757 1.8283 -0.0179 0.06 0.077 -0.0787 -0.02 0.0368 -0.189 0.1008 0.0252 0.1739 -0.018 -0.0209 0.193 0.0124 0.2236 48.863 78.3666 112.9757 5 3.0702 -0.6615 0.2864 0.4007 0.1964 2.2263 0.0971 0.2054 -0.0418 -0.329 -0.1 0.0137 0.0177 -0.0604 -0.0046 0.4304 0.0391 -0.0368 0.2096 0.0358 0.227 31.9225 83.993 69.5924 6 5.0536 1.0813 -3.3291 8.2982 -1.1657 2.8161 -0.519 0.1104 -0.7044 0.3195 0.0382 0.3958 0.711 -0.0529 0.4629 0.6335 0.0392 -0.0884 0.3736 -0.0822 0.3886 14.7894 68.9665 73.3765 7 3.4971 -0.048 -5.3645 4.9335 1.0576 8.4612 -0.051 0.1907 0.0676 0.5466 0.1972 0.0843 -0.382 -0.927 -0.1476 0.9307 0.0725 0.0166 0.8889 0.013 0.8269 40.9952 67.2485 66.7234 8 0.7538 -0.2446 0.5368 1.4154 -0.3209 1.5587 0.0712 -0.0185 0.0262 -0.1512 -0.0412 -0.0319 -0.1057 0.0048 -0.0248 0.3026 -0.0102 -0.029 0.2366 0.0407 0.2294 37.0675 83.6655 83.6677 9 3.0648 0.0674 -1.1958 0.7441 0.2523 2.533 -0.0827 -0.1905 -0.055 0.0774 0.0196 0.0914 0.0309 0.0309 0.0639 0.1487 0.0208 0.0059 0.1846 0.0316 0.2646 21.8313 33.8913 145.4922 10 1.8939 -2.4351 0.4502 5.8848 -1.1884 3.0941 0.1365 0.0967 0.2381 -0.2713 -0.1105 -0.3359 -0.4034 0.0814 -0.0093 0.2075 -0.0211 0.0661 0.2563 -0.004 0.3989 5.613 47.6693 136.7319 11 5.7561 -6.9713 5.131 9.0377 -6.5542 4.7862 1.002 0.0158 0.0334 -0.396 0.5486 0.9615 0.4727 -0.6918 -1.4969 1.0187 0.1225 -0.092 1.0795 0.0612 1.0228 27.6649 51.6092 149.8199 12 1.2999 0.2805 -0.798 1.3136 -0.2636 1.1077 -0.0833 -0.0247 -0.0461 -0.0424 0.059 0.1187 0.0961 -0.0105 0.0231 0.1718 0.0106 -0.0122 0.2138 0.0087 0.2603 31.0488 34.4079 133.671 13 1.5371 0.4215 -0.3337 1.0821 0.3999 2.2292 -0.115 0.0843 -0.1528 -0.5012 0.015 -0.2883 0.4524 0.4448 0.0789 0.445 0.0993 0.0895 0.3112 0.0089 0.2526 62.7018 42.421 99.613 14 4.9587 0.8275 2.1537 2.3121 0.0758 2.312 0.3181 -0.1199 -1.7432 -0.5796 -0.0924 -0.6395 1.2601 0.147 -0.2319 1.2685 0.1014 0.2703 0.5084 0.0071 1.0157 62.7219 20.7316 93.0261 15 2.7928 -3.2497 -2.5545 7.1414 0.6984 7.5234 -0.089 -0.0169 0.1208 -1.0147 0.8156 -1.1694 1.5179 0.4359 -0.6878 1.3226 0.2559 0.2256 1.174 0.2297 1.1911 74.775 34.254 112.6002 16 0.6605 0.2655 -0.4348 1.5306 -0.7475 1.2973 -0.0773 0.0287 -0.0538 -0.3913 0.0113 -0.0083 0.3529 0.077 0.0463 0.3032 0.0363 0.0071 0.2088 -0.0195 0.1993 51.5493 40.6806 109.6462
精密化 TLSグループ 大きな表を表示 (6 x 16) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 (chain A and resid 1:107)A1 - 107 2 X-RAY DIFFRACTION 2 (chain A and resid 108:193)A108 - 193 3 X-RAY DIFFRACTION 3 (chain A and resid 194:206)A194 - 206 4 X-RAY DIFFRACTION 4 (chain A and resid 207:423)A207 - 423 5 X-RAY DIFFRACTION 5 (chain B and resid 1:107)B1 - 107 6 X-RAY DIFFRACTION 6 (chain B and resid 108:193)B108 - 193 7 X-RAY DIFFRACTION 7 (chain B and resid 194:206)B194 - 206 8 X-RAY DIFFRACTION 8 (chain B and resid 207:423)B207 - 423 9 X-RAY DIFFRACTION 9 (chain C and resid 1:107)C1 - 107 10 X-RAY DIFFRACTION 10 (chain C and resid 108:193)C108 - 193 11 X-RAY DIFFRACTION 11 (chain C and resid 194:206)C194 - 206 12 X-RAY DIFFRACTION 12 (chain C and resid 207:423)C207 - 423 13 X-RAY DIFFRACTION 13 (chain D and resid 1:107)D1 - 107 14 X-RAY DIFFRACTION 14 (chain D and resid 108:193)D108 - 193 15 X-RAY DIFFRACTION 15 (chain D and