ソフトウェア 名称 バージョン 分類 REFMAC5.8.0419精密化 HKL-2000データ削減 HKL-2000データスケーリング MOLREP位相決定
精密化 構造決定の手法 : 分子置換開始モデル : PDB entry 7MLH解像度 : 3.05→39.577 Å / Cor.coef. Fo :Fc : 0.94 / Cor.coef. Fo :Fc free : 0.9 / WRfactor Rfree : 0.237 / WRfactor Rwork : 0.182 / SU B : 48.767 / SU ML : 0.376 / Average fsc free : 0.9575 / Average fsc work : 0.974 / 交差検証法 : FREE R-VALUE / ESU R Free : 0.446 / 詳細 : Hydrogens have been added in their riding positionsRfactor 反射数 %反射 Rfree 0.2477 1353 5.077 % Rwork 0.1967 25298 - all 0.199 - - obs - 26651 98.532 %
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 / 溶媒モデル : MASK BULK SOLVENT原子変位パラメータ Biso mean : 68.809 Å2 Baniso -1 Baniso -2 Baniso -3 1- -1.691 Å2 0 Å2 -1.523 Å2 2- - 6.208 Å2 0 Å2 3- - - -3.158 Å2
精密化ステップ サイクル : LAST / 解像度 : 3.05→39.577 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8356 0 0 59 8415
拘束条件 大きな表を表示 (5 x 33) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.005 0.012 8557 X-RAY DIFFRACTION r_bond_other_d0.001 0.016 7834 X-RAY DIFFRACTION r_angle_refined_deg1.302 1.799 11682 X-RAY DIFFRACTION r_angle_other_deg0.448 1.734 18185 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.291 5 1123 X-RAY DIFFRACTION r_dihedral_angle_2_deg8.174 5 20 X-RAY DIFFRACTION r_dihedral_angle_3_deg11.907 10 1319 X-RAY DIFFRACTION r_dihedral_angle_6_deg13.338 10 310 X-RAY DIFFRACTION r_chiral_restr0.057 0.2 1339 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 9975 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 1765 X-RAY DIFFRACTION r_nbd_refined0.205 0.2 1314 X-RAY DIFFRACTION r_symmetry_nbd_other0.218 0.2 7076 X-RAY DIFFRACTION r_nbtor_refined0.174 0.2 4118 X-RAY DIFFRACTION r_symmetry_nbtor_other0.084 0.2 4231 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.226 0.2 228 X-RAY DIFFRACTION r_symmetry_xyhbond_nbd_other0.024 0.2 3 X-RAY DIFFRACTION r_symmetry_nbd_refined0.256 0.2 18 X-RAY DIFFRACTION r_nbd_other0.27 0.2 51 X-RAY DIFFRACTION r_symmetry_xyhbond_nbd_refined0.431 0.2 3 X-RAY DIFFRACTION r_mcbond_it2.078 2.517 4510 X-RAY DIFFRACTION r_mcbond_other2.078 2.517 4510 X-RAY DIFFRACTION r_mcangle_it3.576 4.517 5627 X-RAY DIFFRACTION r_mcangle_other3.576 4.517 5628 X-RAY DIFFRACTION r_scbond_it2.02 2.593 4047 X-RAY DIFFRACTION r_scbond_other2.02 2.593 4046 X-RAY DIFFRACTION r_scangle_it3.465 4.699 6055 X-RAY DIFFRACTION r_scangle_other3.465 4.699 6056 X-RAY DIFFRACTION r_lrange_it7.535 30.032 33760 X-RAY DIFFRACTION r_lrange_other7.535 30.031 33761 X-RAY DIFFRACTION r_ncsr_local_group_10.144 0.05 5882 X-RAY DIFFRACTION r_ncsr_local_group_20.128 0.05 3548 X-RAY DIFFRACTION r_ncsr_local_group_30.118 0.05 6322
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Refine-ID タイプ Rms dev position (Å)Weight position 1 1 EX-RAY DIFFRACTION Local ncs0.14434 0.05008 1 2 EX-RAY DIFFRACTION Local ncs0.14434 0.05008 2 3 EX-RAY DIFFRACTION Local ncs0.1277 0.05008 2 4 EX-RAY DIFFRACTION Local ncs0.1277 0.05008 3 5 EX-RAY DIFFRACTION Local ncs0.11835 0.05009 3 6 EX-RAY DIFFRACTION Local ncs0.11835 0.05009
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 20
大きな表を表示 (11 x 20) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Rfactor all Num. reflection all Fsc free Fsc work % reflection obs (%)WRfactor Rwork 3.05-3.129 0.428 90 0.32 1736 0.325 1989 0.912 0.951 91.8049 0.286 3.129-3.214 0.321 101 0.279 1790 0.281 1913 0.943 0.96 98.85 0.245 3.214-3.306 0.247 96 0.246 1766 0.246 1874 0.959 0.968 99.3597 0.219 3.306-3.407 0.258 96 0.236 1689 0.237 1801 0.965 0.969 99.1116 0.209 3.407-3.518 0.318 85 0.23 1671 0.234 1782 0.947 0.971 98.541 0.203 3.518-3.641 0.305 72 0.235 1622 0.238 1724 0.941 0.968 98.2599 0.213 3.641-3.777 0.275 89 0.236 1543 0.238 1634 0.949 0.968 99.8776 0.215 3.777-3.93 0.28 94 0.211 1495 0.215 1591 0.944 0.973 99.8743 0.187 3.93-4.103 0.282 85 0.187 1458 0.192 1544 0.956 0.978 99.9352 0.174 4.103-4.301 0.221 71 0.168 1368 0.171 1445 0.973 0.983 99.5848 0.157 4.301-4.53 0.162 78 0.143 1323 0.144 1409 0.984 0.988 99.4322 0.134 4.53-4.801 0.184 46 0.148 1247 0.149 1304 0.978 0.988 99.1564 0.141 4.801-5.127 0.18 58 0.146 1158 0.148 1242 0.983 0.988 97.9066 0.143 5.127-5.53 0.183 53 0.152 1093 0.154 1167 0.98 0.987 98.2005 0.145 5.53-6.046 0.23 36 0.164 1013 0.166 1052 0.973 0.984 99.7148 0.158 6.046-6.74 0.245 59 0.198 926 0.2 986 0.963 0.977 99.8986 0.193 6.74-7.746 0.279 53 0.193 820 0.199 878 0.959 0.977 99.4305 0.196 7.746-9.397 0.175 33 0.172 695 0.172 737 0.979 0.982 98.7788 0.181 9.397-12.93 0.22 36 0.172 533 0.176 582 0.976 0.985 97.7663 0.187 12.93-39.577 0.317 22 0.272 349 0.275 373 0.942 0.962 99.4638 0.303
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 12) 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 3.1703 1.1036 1.0042 4.7563 0.6419 1.4704 -0.2171 0.0057 0.0745 0.1294 0.051 -0.22 -0.0661 0.1412 0.1661 0.8293 0.1055 0.1221 0.0394 -0.0227 0.437 31.065 82.834 55.461 2 3.7943 0.4886 0.51 5.3849 0.5827 2.2151 0.055 -0.4112 -0.1906 0.8328 -0.3607 0.2068 0.3254 0.0263 0.3057 0.9219 0.0307 0.1706 0.0752 0.0242 0.3891 26.985 80.491 60.91 3 1.5241 0.5691 -0.2663 4.6745 -0.3544 1.9478 0.0982 -0.3026 0.1525 0.2342 -0.004 -0.3394 0.1357 0.0481 -0.0941 0.8059 -0.006 0.1632 0.1188 -0.2128 0.6413 28.388 116.986 56.978 4 5.9879 -1.0495 -1.8529 1.7271 0.7174 2.6391 -0.064 -0.4696 -0.0662 0.1878 -0.1125 -0.1904 -0.0575 0.1984 0.1765 0.7587 -0.018 0.1857 0.0672 0.0561 0.4715 6.709 146.11 60.447 5 1.5013 -2.0304 0.2252 3.0035 -0.3402 0.0529 -0.1434 0.0774 -0.1317 0.3768 0.0704 0.1928 -0.0254 -0.0238 0.0731 0.9334 0.0175 0.2284 0.1387 -0.0784 0.632 7.541 111.149 54.54 6 3.013 -0.1118 1.157 3.2671 -1.1935 3.8372 0.0477 0.15 0.0106 -0.2113 -0.1528 -0.0111 -0.1978 0.2199 0.1051 0.7744 -0.0016 0.2649 0.0442 -0.0524 0.4111 -1.78 140.705 46.9 7 3.4823 -2.9216 0.8048 22.9499 14.2155 11.0829 -0.7746 -0.1197 -0.2767 0.5887 0.4086 0.9526 -0.06 0.3065 0.366 1.0339 0.0495 0.1813 0.284 -0.0394 0.7086 30.956 91.749 37.745 8 3.6915 -1.3512 -0.2354 3.5435 0.1964 1.16 0.1122 -0.1529 0.4487 -0.1802 -0.1817 -0.1636 -0.1913 -0.1601 0.0695 0.8641 -0.0234 0.1484 0.0525 -0.0699 0.6826 36.208 97.819 30.163 9 1.0109 0.965 0.0477 1.3827 0.2353 0.669 0.0516 0.0108 -0.0265 0.1216 -0.002 -0.103 0.0905 0.0781 -0.0496 0.8923 0.0479 0.1641 0.0165 -0.0302 0.6038 30.424 54.788 29.774 10 2.6575 1.0681 3.4036 3.4191 1.8713 7.2706 -0.0596 0.859 0.1052 0.1364 -0.0343 -0.5479 -0.1232 0.955 0.094 0.7125 -0.05 0.1982 0.3435 0.0222 0.628 20.382 32.439 17.5 11 1.0918 1.5837 0.1148 2.4623 -0.0792 0.4099 -0.1291 -0.0032 0.1163 -0.0892 0.0403 0.186 -0.0277 -0.0775 0.0888 0.8149 0.0157 0.1895 0.0176 -0.0465 0.5607 15.935 67.496 24.093 12 4.2445 1.0604 -0.9339 4.8465 -2.2765 1.7381 -0.0989 -0.0935 -0.1188 0.0799 -0.0821 0.0836 -0.0248 -0.0101 0.1809 0.8031 -0.0127 0.1791 0.0129 -0.0561 0.3823 4.269 37.46 25.621
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 9 ALLE1 - 138 2 X-RAY DIFFRACTION 10 ALLE139 - 210