ソフトウェア 名称 バージョン 分類 MAR345dtbデータ収集 PHASER位相決定 REFMAC5.6.0119精密化 XDSデータ削減 XDSデータスケーリング
精密化 構造決定の手法 : 分子置換開始モデル : PDB ENTRY 2QPN解像度 : 1.898→20 Å / Cor.coef. Fo :Fc : 0.939 / Cor.coef. Fo :Fc free : 0.902 / 交差検証法 : THROUGHOUT / ESU R : 0.038 / ESU R Free : 0.033 / 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 0.23168 1988 5.1 % RANDOM Rwork 0.19202 - - - obs 0.19398 37055 94.51 % - all - 39043 - -
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 : BABINET MODEL WITH MASK原子変位パラメータ Biso mean : 18.058 Å2 Baniso -1 Baniso -2 Baniso -3 1- -8.19 Å2 0 Å2 0 Å2 2- - -5.71 Å2 0 Å2 3- - - 13.9 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.898→20 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4041 0 24 264 4329
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_d0.01 0.019 4252 X-RAY DIFFRACTION r_bond_other_d0 0.02 2926 X-RAY DIFFRACTION r_angle_refined_deg1.377 1.963 5783 X-RAY DIFFRACTION r_angle_other_deg4.247 3.001 7136 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.97 5 570 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.201 23.548 186 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.066 15 751 X-RAY DIFFRACTION r_dihedral_angle_4_deg18.342 15 39 X-RAY DIFFRACTION r_chiral_restr0.078 0.2 662 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.02 4815 X-RAY DIFFRACTION r_gen_planes_other0.007 0.02 876 X-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
LS精密化 シェル 解像度 : 1.898→1.947 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.3 129 - Rwork 0.26 2550 - obs - - 89.9 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 22) 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 4.4527 -0.1077 3.136 3.3726 3.4724 5.9517 0.0789 -0.181 -0.262 0.0516 0.0966 -0.0117 0.1145 -0.0132 -0.1755 0.102 -0.0344 0.0039 0.0655 0.0836 0.2865 55.804 -0.424 75.479 2 1.7758 -0.4471 -0.2388 1.7567 0.8723 0.4359 -0.007 0.0821 0.1047 0.0497 0.0601 -0.12 0.028 0.0387 -0.0532 0.1403 -0.0108 -0.0028 0.0494 0.034 0.1873 52.785 11.747 66.102 3 3.053 -1.0346 0.7365 16.7583 0.8009 0.2507 -0.1674 0.2143 0.092 0.0861 0.1575 -0.0567 -0.0557 0.0892 0.0098 0.1315 -0.0614 0.0274 0.1183 -0.0026 0.2608 38.652 22.549 57.166 4 1.8883 1.1138 0.0804 2.1208 0.6319 0.6998 -0.0373 0.1419 0.1101 0.033 0.043 0.0513 0.0446 -0.0946 -0.0058 0.1137 -0.018 -0.0107 0.0721 0.0189 0.1799 26.668 17.06 52.908 5 0.7819 -0.2825 0.2644 0.2945 0.2134 0.8743 -0.1055 0.1275 0.1108 -0.0502 -0.0243 0.0361 -0.0315 0.0588 0.1297 0.1462 -0.0175 -0.0288 0.0656 0.0263 0.2103 39.365 17.162 52.769 6 3.4638 1.2024 0.094 4.2173 0.7418 1.9147 0.0053 0.3131 -0.1404 -0.0374 -0.0087 0.0378 0.2603 0.1991 0.0034 0.1107 0.0115 -0.0078 0.0775 0.027 0.1584 47.037 7.865 51.76 7 0.1632 -0.3046 0.1738 1.0622 -0.3226 0.1954 -0.0496 -0.0065 0.021 -0.0006 0.029 0.034 -0.0832 0.0153 0.0205 0.139 -0.0423 0.0058 0.0811 0.007 0.2379 45.376 21.924 64.863 8 1.7453 -0.2863 0.3737 2.0569 -0.7135 0.4191 0.0343 -0.1782 -0.0673 0.1331 -0.0604 0.0284 -0.0188 -0.0448 0.0262 0.1335 -0.0124 0.0076 0.0845 0.0226 0.1551 37.382 12.662 74.245 9 1.0145 -0.4823 -0.2545 1.3093 -0.1214 0.525 0.0108 -0.0955 -0.0641 0.0946 0.082 -0.0001 0.0815 -0.0027 -0.0929 0.1024 -0.0106 0.0052 0.0551 0.0146 0.1875 45.296 8.772 69.106 10 4.9455 3.5563 2.5549 5.4259 1.2509 1.4464 0.0421 -0.0988 -0.1933 -0.0436 0.0204 -0.155 0.0201 -0.0645 -0.0625 0.1293 -0.0005 -0.0004 0.0451 0.0397 0.2698 42.499 -2.01 71.726 11 10.5533 -1.5439 -1.909 9.9888 -4.0398 2.2931 -0.295 -0.1772 0.2913 0.2518 0.4886 0.0693 -0.0101 -0.2835 -0.1936 0.2069 -0.085 -0.0554 0.4364 0.2129 0.2796 50.577 9.248 82.066 12 2.1542 1.1462 -0.2221 2.3221 -0.616 0.1864 -0.0889 0.1426 -0.0829 0.0108 0.1417 0.0432 -0.0087 -0.0605 -0.0528 0.1385 -0.0197 0.0055 0.0698 -0.0026 0.2295 -4.421 4.04 61.2 13 1.7433 2.2729 -0.7658 3.9134 -1.1754 0.3696 -0.0151 0.0386 0.1033 0.0077 0.0323 -0.0394 -0.0025 -0.0133 -0.0172 0.12 -0.0261 0.0053 0.0485 -0.0221 0.2303 5.793 14.732 72.775 14 9.5489 -2.9276 6.7896 4.9245 -1.9329 4.8334 -0.2565 -0.2353 0.2795 0.0601 0.058 0.1803 -0.1831 -0.1668 0.1985 0.098 -0.0148 0.051 0.0179 -0.0376 0.3975 17.884 31.997 72.557 15 1.5997 -1.3332 0.2799 2.8812 -0.6789 1.496 0.154 -0.2581 0.088 -0.0392 -0.2433 0.0627 0.2037 0.1385 0.0894 0.1447 -0.049 0.0043 0.2321 -0.0324 0.2095 25.011 15.176 81.053 16 1.6383 0.2822 -0.2578 0.6768 0.4662 0.4585 0.1036 -0.1823 0.0836 -0.0097 -0.0892 0.0315 -0.0376 -0.0069 -0.0145 0.1035 -0.0204 -0.0075 0.0917 -0.0159 0.2027 23.893 18.266 75.028 17 4.5136 -0.1469 0.897 1.6419 0.2215 0.5887 0.0661 -0.4288 0.2809 0.2131 -0.0969 0.0928 0.0032 -0.0314 0.0308 0.1234 -0.0347 0.0195 0.0766 -0.0504 0.229 7.107 19.649 79.666 18 1.1413 0.9212 -0.4696 1.1586 0.8599 4.6861 0.146 -0.1912 0.1453 0.0389 -0.1972 0.2527 0.0896 -0.0392 0.0513 0.2407 0.0017 -0.0932 0.0828 -0.0078 0.3287 0.288 13.738 73.502 19 3.5438 0.8244 1.2938 0.9367 1.8272 4.1858 0.0352 0.3049 0.5881 -0.1482 0.1119 -0.0599 0.1361 -0.0364 -0.1471 0.3855 -0.1789 0.029 0.1278 0.0337 0.3303 10.504 26.664 60.737 20 1.7226 2.6637 -0.4634 5.664 0.9356 2.0565 -0.1093 0.0754 -0.0599 -0.1397 0.1253 0.0593 0.0137 -0.0061 -0.016 0.0888 -0.0215 0.0257 0.0289 -0.0022 0.2661 14.971 11.216 60.921 21 1.4466 0.5258 0.3424 0.9142 0.7879 1.595 -0.0314 0.086 -0.0096 -0.0999 0.0468 -0.0534 -0.1375 -0.0021 -0.0154 0.0918 -0.001 0.0053 0.0449 -0.0029 0.2277 8.547 9.477 60.188 22 1.8009 -0.1105 0.379 1.2181 -1.2137 2.8694 0.015 0.05 -0.1357 -0.1085 -0.0094 -0.0227 0.3237 -0.0362 -0.0055 0.0837 -0.0405 -0.0088 0.0307 -0.0154 0.262 4.753 1.789 62.618
精密化 TLSグループ 大きな表を表示 (5 x 22) 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 - 39 2 X-RAY DIFFRACTION 2 A40 - 66 3 X-RAY DIFFRACTION 3 A67 - 78 4 X-RAY DIFFRACTION 4 A79 - 119 5 X-RAY DIFFRACTION 5 A120 - 149 6 X-RAY DIFFRACTION 6 A150 - 174 7 X-RAY DIFFRACTION 7 A175 - 203 8 X-RAY DIFFRACTION 8 A204 - 228 9 X-RAY DIFFRACTION 9 A229 - 261 10 X-RAY DIFFRACTION 10 A262 - 275 11 X-RAY DIFFRACTION 11 A276 - 284 12 X-RAY DIFFRACTION 12 B19 - 55 13 X-RAY DIFFRACTION 13 B56 - 74 14 X-RAY DIFFRACTION 14 B75 - 87 15 X-RAY DIFFRACTION 15 B88 - 104 16 X-RAY DIFFRACTION 16 B105 - 132 17 X-RAY DIFFRACTION 17 B133 - 166 18 X-RAY DIFFRACTION 18 B167 - 188 19 X-RAY DIFFRACTION 19 B189 - 201 20 X-RAY DIFFRACTION 20 B202 - 220 21 X-RAY DIFFRACTION 21 B221 - 249 22 X-RAY DIFFRACTION 22 B250 - 283