ソフトウェア 名称 バージョン 分類 ADSCQuantumデータ収集 PHASER位相決定 REFMAC5.5.0109精密化 XDSデータ削減 XSCALE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 : 3T4J解像度 : 1.53→19.82 Å / Cor.coef. Fo :Fc : 0.965 / Cor.coef. Fo :Fc free : 0.962 / SU B : 2.993 / SU ML : 0.05 / 交差検証法 : THROUGHOUT / ESU R Free : 0.074 / 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 0.20006 4718 5 % RANDOM Rwork 0.17963 - - - all 0.18065 89986 - - obs 0.18065 89986 99.99 % -
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 : 1.4 Å / 溶媒モデル : MASK原子変位パラメータ Biso mean : 21.379 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.54 Å2 0.27 Å2 0 Å2 2- - 0.54 Å2 0 Å2 3- - - -0.82 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.53→19.82 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4209 0 39 575 4823
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_d0.011 0.022 4591 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 3133 X-RAY DIFFRACTION r_angle_refined_deg1.383 1.958 6265 X-RAY DIFFRACTION r_angle_other_deg0.888 3 7631 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.549 5 592 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.573 23.693 241 X-RAY DIFFRACTION r_dihedral_angle_3_deg12.704 15 797 X-RAY DIFFRACTION r_dihedral_angle_4_deg14.32 15 40 X-RAY DIFFRACTION r_chiral_restr0.086 0.2 686 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.021 5203 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 981 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_it0.657 1.5 2747 X-RAY DIFFRACTION r_mcbond_other0.213 1.5 1094 X-RAY DIFFRACTION r_mcangle_it1.124 2 4479 X-RAY DIFFRACTION r_scbond_it1.908 3 1844 X-RAY DIFFRACTION r_scangle_it2.96 4.5 1750 X-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 : 1.53→1.57 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.303 329 - Rwork 0.258 6528 - obs - - 99.91 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 18) 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 3.9091 2.4931 1.486 16.8506 -8.5723 6.5567 0.362 -0.5112 0.1365 1.7808 -0.5307 -0.0499 -0.7479 0.1607 0.1687 0.4608 0.125 0.0258 1.2161 0.1342 0.158 -4.237 7.436 66.789 2 0.2259 0.0743 -0.9707 0.0943 -1.2396 18.5602 -0.044 -0.106 -0.0593 0.0013 -0.0344 0.0104 0.2403 -0.0547 0.0784 0.0952 -0.0218 0.0143 0.2187 0.0283 0.1242 -5.153 9.968 35.275 3 2.006 0.4791 0.3192 1.0599 0.0564 1.1728 0.0795 -0.0312 0.1121 -0.0554 -0.0781 0.0786 -0.0766 -0.2416 -0.0015 0.0561 0.0449 0.0043 0.162 0.0241 0.1123 -3.534 19.662 15.7 4 4.2256 -1.1489 1.1462 4.4304 0.5733 10.5039 0.0019 0.016 0.1837 -0.0853 -0.063 -0.0652 -0.4929 0.1374 0.0611 0.0949 0.0191 0.022 0.1004 0.031 0.1382 10.8 29.557 10.746 5 2.1916 0.3531 -0.3947 1.6955 0.2086 1.8912 0.0211 -0.1247 0.1614 0.1361 -0.0396 -0.148 -0.1636 0.1081 0.0184 0.0453 0.0181 0.0048 0.1442 0.0148 0.0857 10.542 22.16 19.979 6 2.1483 -0.9217 -1.4527 2.2537 1.7868 4.3915 0.0537 -0.0098 -0.1154 0.1248 -0.078 0.0977 0.1067 -0.055 0.0244 0.0177 0.0137 0.0055 0.1309 0.0606 0.1006 7.194 13.398 22.49 7 10.2923 7.2252 -12.5442 6.0454 -7.9545 16.0426 0.4974 0.0494 0.4804 0.3891 -0.0448 0.4677 -0.5811 -0.166 -0.4526 0.1593 0.0014 0.0465 0.3014 0.018 0.1847 -6.318 21.046 44.333 8 7.7031 -2.5903 -5.3293 3.9512 3.1966 6.4472 0.0364 -0.486 0.3027 0.2497 0.0589 -0.2358 0.011 0.4208 -0.0953 0.166 -0.015 0.001 0.3116 0.0481 0.1415 7.715 15.704 45.713 9 6.8846 -21.7687 -11.8553 120.5805 -13.8819 71.7576 -0.1389 -0.4644 2.0597 1.1821 4.8364 -4.7953 0.1951 -2.7168 -4.6975 1.2717 0.9475 -0.4567 2.8287 -0.9362 1.8892 5.948 18.284 59.084 10 3.8455 -0.5895 -4.9138 0.8195 0.7566 11.2579 -0.0064 -0.4253 -0.1041 0.2047 -0.0607 -0.1227 0.3841 0.3892 0.0671 0.1085 -0.012 0.004 0.2815 0.0775 0.1324 4.903 9.58 45.144 11 5.551 0.0175 0.6036 7.121 -5.2804 14.2904 0.0854 -0.5538 -0.3533 0.5613 0.1179 0.23 0.2782 -0.2211 -0.2033 0.1732 0.0189 -0.0291 0.2602 0.0426 0.1257 -16.425 -11.875 52.826 12 0.2854 -0.56 0.4037 10.7021 -11.0845 11.6169 -0.0508 -0.079 0.0182 0.2562 -0.1467 -0.2159 -0.2044 0.2211 0.1975 0.1071 0.0114 -0.0329 0.2191 0.0104 0.1044 -16.215 4.599 30.11 13 3.3729 0.1409 0.0128 2.3954 -0.0691 2.4823 0.0827 0.1292 0.0711 -0.1685 -0.1452 -0.1524 -0.0292 0.0884 0.0625 0.0222 0.035 -0.0036 0.1703 0.0201 0.0794 -15.821 10.047 12.769 14 5.0874 -0.4523 0.2371 5.6901 -0.3213 6.0434 0.0125 0.4014 0.1325 -0.6081 0.0083 -0.1196 -0.0633 0.1424 -0.0208 0.093 0.0526 -0.0147 0.2333 -0.0031 0.0678 -32.183 8.868 1.478 15 4.1761 -0.5397 1.7886 1.1622 -0.6596 1.2963 0.0906 0.1014 -0.3371 -0.1056 -0.0034 0.0592 0.2098 -0.0277 -0.0872 0.0855 0.0387 0.0044 0.2117 0.0016 0.0893 -30.415 2.704 8.409 16 2.2845 -1.4575 0.5037 3.4526 -1.2469 2.063 0.0077 -0.0666 0.0814 0.1953 -0.0099 0.0166 -0.0259 0.032 0.0023 0.0278 0.02 -0.0116 0.1962 0.0103 0.0542 -28.553 7.2 21.941 17 5.1808 -1.9867 1.4252 3.3163 -0.8518 2.5056 0.0751 0.0137 -0.5692 0.2622 0.0756 0.3374 0.2633 -0.0939 -0.1507 0.2066 0.0207 -0.0201 0.2473 0.0175 0.1693 -26.443 -9.817 38.014 18 1.9811 -1.5422 2.04 2.5019 -1.8302 4.3062 -0.1618 -0.2485 -0.1523 0.5462 0.2704 0.1688 -0.1609 -0.2482 -0.1087 0.1564 0.0467 0.0099 0.2466 0.0482 0.1241 -26.327 -2.387 37.332
精密化 TLSグループ 大きな表を表示 (5 x 18) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A126 - 135 2 X-RAY DIFFRACTION 2 A136 - 170 3 X-RAY DIFFRACTION 3 A171 - 210 4 X-RAY DIFFRACTION 4 A211 - 228 5 X-RAY DIFFRACTION 5 A229 - 272 6 X-RAY DIFFRACTION 6 A273 - 325 7 X-RAY DIFFRACTION 7 A326 - 339 8 X-RAY DIFFRACTION 8 A340 - 361 9 X-RAY DIFFRACTION 9 A364 - 369 10 X-RAY DIFFRACTION 10 A370 - 393 11 X-RAY DIFFRACTION 11 B127 - 144 12 X-RAY DIFFRACTION 12 B145 - 166 13 X-RAY DIFFRACTION 13 B167 - 206 14 X-RAY DIFFRACTION 14 B207 - 227 15 X-RAY DIFFRACTION 15 B228 - 259 16 X-RAY DIFFRACTION 16 B260 - 333 17 X-RAY DIFFRACTION 17 B334 - 373 18 X-RAY DIFFRACTION 18 B374 - 393