ソフトウェア 名称 バージョン 分類 REFMAC5.2.0019精密化 SBC-Collectデータ収集 HKL-2000データ削減 HKL-2000データスケーリング HKL-3000位相決定 SHELXEモデル構築 SOLVE位相決定 RESOLVE位相決定 ARP/wARPモデル構築
精密化 構造決定の手法 : 多波長異常分散 / 解像度 : 2.3→40 Å / Cor.coef. Fo :Fc : 0.953 / Cor.coef. Fo :Fc free : 0.928 / SU B : 11.217 / SU ML : 0.145 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / σ(I) : 0 / ESU R : 0.232 / ESU R Free : 0.206 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.24284 1328 5.1 % RANDOM Rwork 0.192 - - - all 0.1946 26070 - - obs 0.19456 24692 93.39 % -
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 : 41.639 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.75 Å2 0 Å2 0 Å2 2- - 0.97 Å2 0 Å2 3- - - -1.72 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.3→40 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2964 0 0 157 3121
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_d0.019 0.022 3032 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.613 1.961 4100 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg7.687 5 358 X-RAY DIFFRACTION r_dihedral_angle_2_deg35.61 24.967 151 X-RAY DIFFRACTION r_dihedral_angle_3_deg17.584 15 534 X-RAY DIFFRACTION r_dihedral_angle_4_deg19.915 15 10 X-RAY DIFFRACTION r_chiral_restr0.11 0.2 427 X-RAY DIFFRACTION r_gen_planes_refined0.008 0.02 2314 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refined0.21 0.2 1207 X-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refined0.309 0.2 1999 X-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refined0.255 0.2 179 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.172 0.2 30 X-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refined0.249 0.2 7 X-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it0.784 1.5 1855 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it1.263 2 2901 X-RAY DIFFRACTION r_scbond_it1.988 3 1377 X-RAY DIFFRACTION r_scangle_it2.936 4.5 1199 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
Refine LS restraints NCS Dom-ID : 1 / Auth asym-ID : A / Ens-ID : 1 / 数 : 1427 / Refine-ID : X-RAY DIFFRACTION
タイプ Rms dev position (Å)Weight position medium positional0.37 0.5 medium thermal1.25 2
LS精密化 シェル 解像度 : 2.3→2.36 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.295 49 - Rwork 0.23 1163 - obs - - 60.48 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 29) 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 2.424 -0.664 -1.8271 1.4497 2.2541 3.8027 0.0264 -0.1441 -0.1759 0.1206 -0.0397 0.1185 -0.2239 0.1255 0.0133 0.1972 -0.0254 0.0268 0.024 0.0494 -0.0265 13.8329 0.0987 26.0877 2 2.5568 -1.1255 2.6679 3.7335 1.0984 4.3789 -0.1415 -0.1206 0.2118 0.3317 0.021 0.272 -0.6617 -0.1591 0.1205 0.1527 -0.0135 0.0405 0.0737 0.0349 0.0445 3.7158 12.3465 21.4039 3 2.9785 1.1487 -0.0164 4.8762 -0.8875 7.5449 0.039 0.1328 -0.0906 -0.2343 -0.0607 0.1914 -0.0609 -0.0303 0.0217 0.0993 -0.0207 0.0209 -0.0241 0.026 -0.0272 8.899 5.0391 13.0797 4 1.4535 2.0972 -1.023 14.9489 10.2477 13.0329 -0.2669 0.3018 -0.1879 -0.0716 -0.2945 1.8321 0.5307 -1.1955 0.5614 -0.0144 -0.2586 0.0932 0.3976 0.0245 0.4347 -9.8641 -0.708 21.7918 5 39.258 -5.6725 -10.8974 31.321 -6.989 5.4292 0.5654 2.9061 -0.2226 -5.3828 -0.4869 2.0553 1.7514 -3.2128 -0.0785 0.7153 -0.066 -0.3075 0.3266 0.0619 0.3875 -5.8197 4.7034 8.3222 6 7.8581 -1.5691 2.6992 8.752 -2.7069 9.7201 0.0091 -0.5959 0.389 0.7236 0.3414 1.0289 -0.5516 -1.4 -0.3504 0.0456 -0.0262 0.128 0.1583 -0.0102 0.1484 -5.7464 7.7057 23.5179 7 3.5248 -1.8188 -3.0414 1.7942 3.3057 6.1475 -0.1062 0.1437 -0.3812 -0.0414 -0.3828 0.5283 0.6012 -0.2637 0.489 0.1405 -0.1176 0.0055 0.1033 0.0323 0.0259 6.5234 -0.594 15.3894 8 3.2699 -1.7138 0.0966 4.8092 3.4474 7.1544 -0.0122 -0.4726 0.0239 0.465 -0.2011 0.4164 0.0615 -0.5585 0.2133 0.1627 -0.064 0.1377 0.0552 -0.0199 0.0193 4.7851 7.0514 28.0075 9 5.5449 -1.8132 0.2914 4.5951 0.3845 2.1194 0.122 -0.2511 0.6471 0.5094 -0.2886 -0.0176 -0.508 0.346 0.1666 0.3387 -0.107 0.0263 -0.0229 -0.0088 -0.0059 12.4906 14.5319 28.1126 10 4.9505 -2.434 0.6537 3.9447 -6.6965 14.8759 -0.2073 -0.0013 -0.1181 -0.3284 0.3733 0.2056 0.7082 -0.2579 -0.1659 0.1217 -0.0499 0.0066 0.1291 0.0648 -0.0809 18.5084 -3.4698 14.5961 11 32.0811 -0.8409 -2.9583 4.8582 -5.5732 22.0784 0.0147 -1.4604 -0.817 0.0555 -0.4519 -0.0456 1.2472 0.7597 0.4373 0.1378 0.08 -0.0346 0.0643 0.1157 -0.1551 27.3231 -7.4423 18.5918 12 83.3456 -35.2249 24.4508 30.2266 6.6629 38.2435 0.9698 0.0674 -2.9348 1.0724 -0.3438 -0.4249 2.7493 2.4382 -0.626 0.0666 0.1511 0.1443 0.1117 0.1967 -0.0487 35.7151 -10.393 14.5088 13 13.5522 -8.5809 -2.6832 18.0062 -5.8 10.4038 0.2777 -0.2714 -0.0471 0.0757 -0.2596 -0.3942 0.2461 1.5703 -0.0181 -0.0186 0.0737 0.0249 0.1291 0.0603 -0.2006 31.4014 -1.1167 11.505 14 8.7584 -6.5933 -0.851 5.0284 0.1226 4.215 0.1215 0.1195 0.6916 -0.4686 0.0967 -0.1893 -0.055 0.4734 -0.2182 0.0992 -0.1298 -0.0145 0.0287 0.0492 0.0071 22.1547 10.2381 22.9475 15 31.9709 2.0811 -6.7182 21.1305 -0.2804 1.4129 -0.1552 2.1073 -0.4265 -1.0436 0.2109 0.3473 -0.1602 0.8524 -0.0557 -0.1357 -0.0551 -0.0338 0.123 0.02 -0.1231 38.8551 17.9824 -0.6302 16 33.1111 4.3917 -4.3837 2.8181 2.0607 3.7031 0.3046 -0.9768 -1.1998 1.3497 -0.4009 -0.1446 -0.0808 -0.0378 0.0963 0.0076 -0.0358 -0.0247 -0.0261 0.0407 -0.014 29.0032 13.8184 5.2502 17 0.9956 -1.2968 1.416 2.5134 -0.6581 3.7215 0.0905 -0.3228 -0.0303 -0.0152 0.1474 0.2998 0.3957 -0.1737 -0.2379 0.1009 -0.1008 0.0104 0.2277 0.0306 -0.0484 14.8007 2.457 -1.0677 18 1.2894 -0.8231 -0.789 0.5255 0.5037 0.4828 -0.0987 0.0716 -0.2051 0.4351 0.0684 -0.3502 0.4115 0.0239 0.0303 0.1305 -0.0755 -0.0462 0.1932 0.0208 -0.0423 24.4917 4.757 1.0758 19 1.4579 -0.3522 0.5881 0.3859 -0.1901 1.6325 -0.0557 -0.0549 0.0429 0.0118 -0.0859 -0.0089 0.2646 0.2527 0.1416 0.0602 -0.035 0.0253 0.1244 -0.0004 -0.0549 27.7437 11.9405 -7.5568 20 3.0949 2.2425 -1.608 5.3932 1.2252 2.6952 -0.1201 0.1641 -0.0585 -0.475 0.0388 0.1303 0.1211 0.1371 0.0813 0.0685 -0.0671 0.0039 0.0793 -0.0199 -0.0783 20.749 6.6117 -14.1782 21 7.6366 -6.8284 -1.498 7.1625 1.2869 0.2965 0.2272 -0.1293 0.186 -0.5609 0.0789 -0.2158 -0.1542 -0.4266 -0.3061 -0.0512 0.0235 0.0312 0.0103 -0.0178 -0.024 15.4348 24.3014 -5.4574 22 67.081 -7.7198 -20.5812 2.9887 8.1094 22.0063 -0.6821 5.7769 4.9912 -1.2222 -1.072 0.148 -2.2852 -0.596 1.7541 0.5676 -0.0334 -0.1447 0.3167 0.2169 0.1672 19.9192 21.344 -20.1222 23 7.3816 -0.7365 -4.0258 4.3931 -1.9683 20.219 -0.044 -0.4154 0.6881 -0.1298 0.1572 -0.0508 -0.4933 0.5126 -0.1132 -0.063 -0.0324 -0.0359 -0.0928 -0.0411 -0.1117 21.9584 20.9819 -4.6973 24 1.9181 0.5808 2.5324 1.9663 2.2166 5.3405 -0.2729 -0.0027 0.2637 -0.0665 -0.1005 0.2397 0.3631 -0.2117 0.3734 0.0838 -0.0857 -0.0045 0.0847 -0.0129 -0.0654 15.3551 8.0518 -8.8833 25 24.7507 5.4576 1.8643 4.2228 3.072 2.4855 0.6245 -1.1641 -0.7628 0.5681 -0.6113 -0.3443 0.329 -0.5658 -0.0132 -0.0376 -0.0201 -0.0392 0.1491 0.0596 -0.1825 31.0468 12.9994 8.0829 26 3.0052 3.9985 1.8005 7.7973 2.238 2.0518 -0.0057 0.04 -0.4801 0.2528 0.0672 -0.5364 0.5628 0.0399 -0.0615 0.1033 0.0227 -0.0079 0.0491 0.0194 -0.067 29.6282 2.667 0.5277 27 8.1951 8.6446 -2.3543 9.4155 -0.6347 12.1904 -0.0085 0.3307 0.0654 -0.3755 -0.0981 0.0952 0.3226 -0.7144 0.1067 0.3251 -0.1776 -0.0149 -0.0313 -0.014 -0.1146 12.1448 -3.1737 -13.0294 28 12.4653 3.4611 -6.3851 12.7993 4.1855 13.6733 -0.6455 -0.1734 0.2327 0.593 0.061 0.9675 1.3837 -0.4075 0.5845 0.4749 -0.2163 -0.073 0.1287 0.1105 -0.026 9.3566 -11.8491 -9.9702 29 14.9369 11.3522 0.8109 11.838 2.202 5.3664 -0.3671 0.1833 -1.1846 -0.3176 0.4089 -1.0412 0.787 0.0833 -0.0418 0.2154 0.0664 0.1231 -0.0301 -0.0078 -0.0537 26.0211 -6.727 -3.6248
精密化 TLSグループ 大きな表を表示 (7 x 29) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA12 - 24 12 - 24 2 X-RAY DIFFRACTION 2 AA25 - 43 25 - 43 3 X-RAY DIFFRACTION 3 AA44 - 56 44 - 56 4 X-RAY DIFFRACTION 4 AA57 - 67 57 - 67 5 X-RAY DIFFRACTION 5 AA68 - 83 68 - 83 6 X-RAY DIFFRACTION 6 AA84 - 99 84 - 99 7 X-RAY DIFFRACTION 7 AA100 - 109 100 - 109 8 X-RAY DIFFRACTION 8 AA110 - 124 110 - 124 9 X-RAY DIFFRACTION 9 AA125 - 139 125 - 139 10 X-RAY DIFFRACTION 10 AA140 - 150 140 - 150 11 X-RAY DIFFRACTION 11 AA151 - 158 151 - 158 12 X-RAY DIFFRACTION 12 AA159 - 164 159 - 164 13 X-RAY DIFFRACTION 13 AA165 - 174 165 - 174 14 X-RAY DIFFRACTION 14 AA175 - 188 175 - 188 15 X-RAY DIFFRACTION 15 BB2 - 6 2 - 6 16 X-RAY DIFFRACTION 16 BB7 - 10 7 - 10 17 X-RAY DIFFRACTION 17 BB11 - 21 11 - 21 18 X-RAY DIFFRACTION 18 BB22 - 29 22 - 29 19 X-RAY DIFFRACTION 19 BB30 - 44 30 - 44 20 X-RAY DIFFRACTION 20 BB45 - 56 45 - 56 21 X-RAY DIFFRACTION 21 BB57 - 68 57 - 68 22 X-RAY DIFFRACTION 22 BB69 - 79 69 - 79 23 X-RAY DIFFRACTION 23 BB80 - 100 80 - 100 24 X-RAY DIFFRACTION 24 BB101 - 117 101 - 117 25 X-RAY DIFFRACTION 25 BB118 - 124 118 - 124 26 X-RAY DIFFRACTION 26 BB125 - 140 125 - 140 27 X-RAY DIFFRACTION 27 BB141 - 150 141 - 150 28 X-RAY DIFFRACTION 28 BB151 - 174 151 - 174 29 X-RAY DIFFRACTION 29 BB175 - 188 175 - 188