ソフトウェア 名称 バージョン 分類 REFMAC5.7.0032精密化 SCALA3.3.20データスケーリング PDB_EXTRACT3.15 データ抽出 PHENIX位相決定 XDSデータ削減
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.651→49.11 Å / Cor.coef. Fo :Fc : 0.953 / Cor.coef. Fo :Fc free : 0.923 / WRfactor Rfree : 0.2012 / WRfactor Rwork : 0.1656 / FOM work R set : 0.7996 / SU B : 27.747 / SU ML : 0.241 / SU R Cruickshank DPI : 0.9157 / SU Rfree : 0.291 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.916 / ESU R Free : 0.291 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.2208 719 5.1 % RANDOM Rwork 0.1805 - - - obs 0.1826 13397 96.38 % -
溶媒の処理 イオンプローブ半径 : 1.1 Å / 減衰半径 : 1.1 Å / VDWプローブ半径 : 1.3 Å / 溶媒モデル : MASK原子変位パラメータ Biso max : 163.61 Å2 / Biso mean : 53.166 Å2 / Biso min : 19.33 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.23 Å2 0.23 Å2 -0 Å2 2- - 0.23 Å2 0 Å2 3- - - -0.76 Å2
精密化ステップ サイクル : final / 解像度 : 2.651→49.11 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3098 0 2 10 3110 Biso mean - - 45.53 33.09 - 残基数 - - - - 403
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.007 0.019 3174 X-RAY DIFFRACTION r_bond_other_d0.003 0.02 3063 X-RAY DIFFRACTION r_angle_refined_deg1.096 1.985 4326 X-RAY DIFFRACTION r_angle_other_deg0.999 3 7052 X-RAY DIFFRACTION r_dihedral_angle_1_deg4.764 5 405 X-RAY DIFFRACTION r_dihedral_angle_2_deg33.483 23.769 130 X-RAY DIFFRACTION r_dihedral_angle_3_deg16.064 15 507 X-RAY DIFFRACTION r_dihedral_angle_4_deg18.724 15 22 X-RAY DIFFRACTION r_chiral_restr0.065 0.2 518 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.021 3542 X-RAY DIFFRACTION r_gen_planes_other0.003 0.02 676 X-RAY DIFFRACTION r_mcbond_it5.11 3.216 1614 X-RAY DIFFRACTION r_mcbond_other5.092 3.215 1613 X-RAY DIFFRACTION r_mcangle_it7.279 4.836 2015
Refine LS restraints NCS Ens-ID : 1 / 数 : 27289 / Refine-ID : X-RAY DIFFRACTION / タイプ : interatomic distance / Rms dev position : 0.12 Å / Weight position : 0.05
LS精密化 シェル 解像度 : 2.651→2.719 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.349 42 - Rwork 0.312 814 - all - 856 - obs - - 78.24 %
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 3.5733 -2.3445 -1.1778 5.3322 0.9086 1.4286 0.217 0.0472 0.0421 -0.3581 -0.0272 0.0191 -0.0915 -0.1498 -0.1898 0.1092 0.0667 -0.0154 0.1023 -0.0007 0.0937 28.12 62.317 40.198 2 13.0962 1.4903 1.1735 0.9463 0.3719 0.1816 -0.0895 -0.2184 0.9053 -0.05 0.0529 -0.0979 -0.0306 0.026 0.0366 0.1458 -0.0973 0.0348 0.1763 0.0411 0.2111 55.225 61.821 29.8 3 6.2411 -0.676 -2.7125 1.5932 0.3864 1.1978 -0.1063 0.2422 0.493 -0.1096 0.2696 -0.0289 0.0406 -0.0821 -0.1633 0.0796 0.0038 -0.0069 0.1757 0.0294 0.1912 52.36 61.3 40.055 4 2.2009 -2.7977 0.9901 4.9398 1.1186 4.5345 -0.1459 -0.0575 0.0059 0.0797 -0.0646 0.1228 -0.2119 -0.2581 0.2105 0.1119 -0.0161 -0.0567 0.1491 0.0254 0.1078 38.976 51.602 33.432 5 3.1837 -2.0007 2.1091 1.3384 -2.0232 7.4279 0.1654 0.3015 -0.1867 -0.1219 -0.1585 0.096 0.2277 -0.0686 -0.0069 0.1356 -0.092 0.0528 0.1467 -0.0228 0.1554 58.812 49.032 31.676 6 4.4612 -0.0141 -1.0031 0.8443 0.3091 0.344 0.1505 0.0015 0.1499 0.1576 -0.0133 -0.2052 0.0018 -0.0205 -0.1371 0.1023 0.0297 0.0372 0.1316 0.0048 0.1842 49.536 62.42 47.338 7 6.8131 -6.3077 -1.0187 6.2817 2.2294 3.9694 0.0174 -0.3398 -0.1715 -0.0414 0.299 0.0255 -0.0056 0.0947 -0.3164 0.0913 0.0177 0.0339 0.132 0.0405 0.1492 62.409 55.317 43.104 8 14.0753 -9.431 2.9439 15.1838 -6.3508 2.8004 -0.3269 0.4941 0.9713 -0.3974 0.2463 -0.5779 0.2521 -0.188 0.0806 0.0845 -0.086 -0.0771 0.1102 0.0267 0.3205 64.585 67.253 37.115 9 3.6205 2.172 1.7444 8.216 2.4558 2.9531 -0.0569 0.0378 -0.0347 0.0699 -0.0428 0.239 0.2403 -0.0585 0.0996 0.0761 -0.019 0.006 0.0835 0.004 0.0951 29.675 30.684 42.814 10 2.3213 5.8484 -0.3936 15.6504 -0.6582 0.1991 0.8036 -0.6389 0.0309 1.1991 -1.3526 0.9737 -0.2065 0.145 0.549 0.4692 -0.1812 -0.179 0.1876 0.1047 1.1256 27.33 29.909 51.196 11 8.1587 1.1569 -0.0584 0.1819 0.0946 1.03 0.1696 -0.3513 -0.5857 0.0307 -0.0871 -0.0896 0.1573 -0.0013 -0.0826 0.0955 0.0467 -0.0244 0.1718 0.0044 0.1922 50.483 32.956 56.081 12 1.0825 0.9475 0.6466 0.9516 0.5183 0.4051 0.1905 -0.3067 -0.1087 0.0792 -0.1412 -0.1201 0.1357 -0.2322 -0.0493 0.1695 -0.06 -0.0258 0.2537 0.0008 0.1315 54.89 34.12 47.614 13 3.7834 -3.2527 -1.0245 2.8168 0.5214 8.7496 -0.0775 0.1795 -0.0056 0.09 -0.1839 -0.0023 -0.444 -0.1849 0.2614 0.0835 -0.0548 0.0392 0.1656 -0.0235 0.1344 38.675 42.784 52.093 14 3.9028 2.6065 -1.7996 2.1105 -0.391 2.7033 0.0127 -0.1508 0.1645 -0.0467 -0.0772 0.1746 -0.2271 0.0254 0.0644 0.1251 0.0864 -0.0511 0.1712 -0.013 0.1251 58.069 46.138 55.287 15 6.6914 0.8933 2.4267 0.7901 0.1096 0.9486 -0.1112 0.3371 0.0227 0.0492 0.0975 -0.0074 -0.0596 0.1047 0.0137 0.083 0.0137 0.0391 0.1782 -0.028 0.1215 54.388 34.21 40.419 16 5.1782 0.949 0.9313 7.7337 -1.1121 0.5449 0.1047 -0.2344 -0.5755 0.3322 0.0812 -0.6116 -0.0133 0.0378 -0.1858 0.0608 0.0489 -0.0348 0.111 -0.0692 0.2686 65.531 31.517 50.028
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 A19 - 71 2 X-RAY DIFFRACTION 2 A72 - 94 3 X-RAY DIFFRACTION 3 A95 - 115 4 X-RAY DIFFRACTION 4 A116 - 135 5 X-RAY DIFFRACTION 5 A136 - 163 6 X-RAY DIFFRACTION 6 A164 - 185 7 X-RAY DIFFRACTION 7 A186 - 202 8 X-RAY DIFFRACTION 8 A203 - 220 9 X-RAY DIFFRACTION 9 B20 - 55 10 X-RAY DIFFRACTION 10 B56 - 66 11 X-RAY DIFFRACTION 11 B67 - 91 12 X-RAY DIFFRACTION 12 B92 - 115 13 X-RAY DIFFRACTION 13 B116 - 134 14 X-RAY DIFFRACTION 14 B135 - 162 15 X-RAY DIFFRACTION 15 B163 - 197 16 X-RAY DIFFRACTION 16 B198 - 220