ソフトウェア 名称 バージョン 分類 NB PHASER位相決定 Show REFMAC精密化 Show PDB_EXTRACT3.11 データ抽出 Show Blu-Iceデータ収集 MOSFLMデータ削減 SCALAデータスケーリング
精密化 構造決定の手法 : 分子置換 / 解像度 : 2.1→35.68 Å / Cor.coef. Fo :Fc : 0.952 / Cor.coef. Fo :Fc free : 0.926 / Occupancy max : 1 / Occupancy min : 0.38 / SU B : 8.971 / SU ML : 0.122 / SU R Cruickshank DPI : 0.2084 / 交差検証法 : THROUGHOUT / ESU R : 0.21 / ESU R Free : 0.173 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUTRfactor 反射数 %反射 Selection details Rfree 0.21847 4045 5.1 % RANDOM Rwork 0.17949 - - - obs 0.18146 75078 98.16 % - all - 79123 - -
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原子変位パラメータ Biso mean : 29.191 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.05 Å2 0 Å2 0.32 Å2 2- - 0.46 Å2 0 Å2 3- - - -2 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.1→35.68 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 9184 0 64 799 10047
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_d0.018 0.019 9543 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.919 1.988 12864 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg6.363 5 1196 X-RAY DIFFRACTION r_dihedral_angle_2_deg38.913 25.061 409 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.447 15 1722 X-RAY DIFFRACTION r_dihedral_angle_4_deg16.729 15 29 X-RAY DIFFRACTION r_chiral_restr0.124 0.2 1424 X-RAY DIFFRACTION r_gen_planes_refined0.009 0.02 7089 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refinedX-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refinedX-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refinedX-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refinedX-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refinedX-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_itX-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_itX-RAY DIFFRACTION r_scbond_itX-RAY DIFFRACTION r_scangle_itX-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
Refine LS restraints NCS Ens-ID : 1 / 数 : 2276 / Refine-ID : X-RAY DIFFRACTION / タイプ : TIGHT THERMAL / Weight position : 0.5
Dom-ID Auth asym-ID Rms dev position (Å)1 A1.87 2 B1.79 3 C2.4 4 D1.9
LS精密化 シェル 解像度 : 2.1→2.154 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.257 267 - Rwork 0.21 5560 - obs - - 97.69 %
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 0.5773 -0.0254 0.2202 1.7999 -0.1926 1.4668 0.0118 -0.135 0.0339 0.2888 -0.0666 0.0611 -0.1849 -0.1428 0.0548 0.0817 0.0223 0.0198 0.1275 -0.0769 0.1758 -14.621 3.995 0.188 2 1.2302 -0.6268 0.593 1.5498 -0.1016 1.3019 0.0608 -0.0239 -0.0547 0.2047 -0.0755 -0.0362 0.0208 -0.0294 0.0147 0.0564 -0.0309 0.0095 0.0791 -0.0226 0.1481 -7.804 -11.242 -0.048 3 0.352 0.0006 0.1523 1.2484 0.145 1.2567 0.0085 0.0186 0.0439 0.0822 -0.0331 0.0929 -0.1137 -0.1121 0.0246 0.0215 0.0217 -0.0081 0.0713 -0.0712 0.1598 -12.034 1.813 -14.726 4 8.7553 3.4065 4.3268 4.2665 0.7395 7.038 -0.033 0.0291 0.4012 -0.1473 -0.0648 0.0839 -0.6292 0.0601 0.0978 0.2028 0.0681 -0.0072 0.0536 -0.0541 0.2558 -10.097 20.348 -14.247 5 1.4416 0.2051 -0.1946 1.4193 -0.3797 0.9081 -0.0108 0.1855 -0.1285 -0.2321 -0.083 -0.0636 0.1068 -0.0202 0.0938 0.0843 0.0434 -0.0222 0.1437 -0.1005 0.1213 4.078 -16.085 -48.017 6 1.7056 0.3754 0.1145 1.2843 0.2669 0.8647 0.0857 0.101 0.0625 -0.1435 -0.1502 -0.1062 -0.036 0.0608 0.0645 0.0475 0.0542 -0.0137 0.1097 0.0155 0.0904 8.923 -0.821 -43.315 7 0.7854 0.0049 -0.2766 1.0764 0.0347 0.6192 0.0573 0.1461 -0.0672 -0.0905 -0.1123 0.0841 0.074 -0.111 0.055 0.0372 0.0257 -0.0365 0.0938 -0.0902 0.137 -4.094 -13.906 -35.255 8 9.8047 -2.6439 -1.1539 3.9444 -0.2174 1.6167 -0.2835 -0.1466 -0.5657 0.3392 0.0263 0.1685 0.3031 0.0334 0.2572 0.1599 0.0101 0.0087 0.0849 -0.1117 0.2761 -2.233 -32.437 -34.236 9 1.0519 -0.2869 -0.0221 1.3123 0.1304 1.2069 0.0724 0.1912 -0.0163 -0.1994 -0.169 -0.3933 -0.1135 0.3148 0.0966 0.043 -0.016 0.0339 0.2379 0.1745 0.3895 38.733 -1.331 -36.281 10 0.7309 0.4431 0.4702 1.96 -0.239 1.8665 0.0734 0.0509 -0.0459 -0.1875 -0.2324 -0.3014 0.2186 0.1232 0.159 0.0471 0.0511 0.0436 0.1353 0.0741 0.3068 30.922 -15.762 -33.34 11 0.5472 -0.2353 0.2248 0.9703 -0.1121 1.4355 -0.0117 0.0431 0.0261 0.0938 -0.1432 -0.3209 -0.1396 0.2629 0.1549 0.0269 -0.0559 -0.069 0.1417 0.1641 0.352 36.249 -0.56 -21.238 12 8.9556 -4.8138 9.9342 5.9738 -5.0547 11.8207 -0.5353 0.0819 0.4741 0.5257 0.1044 -0.5805 -1.1503 0.2588 0.4309 0.4861 -0.1477 -0.0732 0.1584 0.1938 0.4764 35.606 17.716 -25.068 13 1.2289 0.1888 0.4453 1.4619 0.2289 0.9613 -0.004 -0.2918 -0.0206 0.399 -0.1073 -0.1024 -0.1092 0.1135 0.1113 0.1695 -0.0886 -0.1201 0.1663 0.1117 0.1899 19.177 -10.805 14.52 14 1.5019 -0.2509 -0.3602 1.3512 -0.442 0.39 0.1018 -0.0528 0.1151 0.3217 -0.1799 -0.0565 -0.2339 0.046 0.0781 0.2071 -0.0811 -0.1227 0.1079 0.0092 0.1775 15.349 3.677 7.168 15 0.784 0.1889 -0.3556 1.1589 -0.0556 0.7208 0.0203 -0.1485 -0.042 0.1793 -0.1608 -0.2626 -0.067 0.2042 0.1405 0.0673 -0.0749 -0.1296 0.1294 0.1522 0.2603 27.406 -11.594 1.666 16 14.7579 3.8302 -1.2105 2.9267 0.012 0.8316 -0.2139 -0.0112 -0.8718 0.1015 -0.0163 -0.5657 0.3912 0.092 0.2302 0.2582 -0.0256 -0.0206 0.0946 0.1632 0.388 24.12 -29.912 3.986
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 A2 - 57 2 X-RAY DIFFRACTION 2 A58 - 167 3 X-RAY DIFFRACTION 3 A168 - 277 4 X-RAY DIFFRACTION 4 A278 - 293 5 X-RAY DIFFRACTION 5 B2 - 57 6 X-RAY DIFFRACTION 6 B58 - 167 7 X-RAY DIFFRACTION 7 B168 - 277 8 X-RAY DIFFRACTION 8 B278 - 293 9 X-RAY DIFFRACTION 9 C2 - 57 10 X-RAY DIFFRACTION 10 C58 - 167 11 X-RAY DIFFRACTION 11 C168 - 277 12 X-RAY DIFFRACTION 12 C278 - 293 13 X-RAY DIFFRACTION 13 D2 - 57 14 X-RAY DIFFRACTION 14 D58 - 167 15 X-RAY DIFFRACTION 15 D168 - 277 16 X-RAY DIFFRACTION 16 D278 - 293