ソフトウェア 名称 バージョン 分類 XDSVERSION Jan 26, 2018データ削減 XSCALEデータスケーリング REFMAC5.8.0267精密化 PDB_EXTRACT3.27 データ抽出 CRANK2位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.2→47.12 Å / Cor.coef. Fo :Fc : 0.952 / Cor.coef. Fo :Fc free : 0.931 / SU B : 16.16 / SU ML : 0.215 / 交差検証法 : THROUGHOUT / ESU R : 0.309 / ESU R Free : 0.225 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLYRfactor 反射数 %反射 Selection details Rfree 0.2557 7063 5 % RANDOM Rwork 0.2183 - - - obs 0.2202 134180 97.75 % -
溶媒の処理 イオンプローブ半径 : 0.7 Å / 減衰半径 : 0.7 Å / VDWプローブ半径 : 1 Å / 溶媒モデル : MASK原子変位パラメータ Biso max : 266.64 Å2 / Biso mean : 91.005 Å2 / Biso min : 26.4 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.65 Å2 -0.77 Å2 2.89 Å2 2- - -0.87 Å2 -0.07 Å2 3- - - -0.86 Å2
精密化ステップ サイクル : final / 解像度 : 2.2→47.12 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 17734 1986 56 630 20406 Biso mean - - 69.1 51.61 - 残基数 - - - - 2349
拘束条件 大きな表を表示 (5 x 28) 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 0.017 20459 X-RAY DIFFRACTION r_bond_other_d0.001 0.019 18587 X-RAY DIFFRACTION r_angle_refined_deg1.014 1.797 27982 X-RAY DIFFRACTION r_angle_other_deg1.013 2.661 42754 X-RAY DIFFRACTION r_dihedral_angle_1_deg4.997 5 2259 X-RAY DIFFRACTION r_dihedral_angle_2_deg29.52 20.188 1064 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.697 15 3197 X-RAY DIFFRACTION r_dihedral_angle_4_deg16.46 15 202 X-RAY DIFFRACTION r_chiral_restr0.06 0.2 3029 X-RAY DIFFRACTION r_gen_planes_refined0.003 0.02 21685 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 4899 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_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
LS精密化 シェル 解像度 : 2.2→2.257 Å / Rfactor Rfree error : 0 / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.405 514 - Rwork 0.369 9760 - all - 10274 - obs - - 96.36 %
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 0.4146 -0.3814 0.3896 4.2885 0.2337 0.7484 -0.0132 -0.0528 -0.0797 0.1051 0.1599 0.2137 0.1553 -0.0085 -0.1467 0.3193 0.085 -0.1063 0.0443 -0.0627 0.268 -9.494 43.417 100.742 2 1.0108 -3.7136 1.18 14.0673 -4.1217 2.456 -0.0268 0.1528 0.2891 0.2999 -0.5577 -1.2645 -0.4069 0.267 0.5845 0.493 -0.0422 -0.1246 0.2766 -0.0265 0.4678 -3.057 81.096 85.642 3 1.6535 3.0006 0.0473 12.1111 8.4371 10.5337 0.5845 -0.0909 0.1478 0.1099 -0.4052 0.0517 -1.1418 -0.518 -0.1793 0.8018 0.1135 -0.0246 0.7266 -0.0321 0.8922 8.906 77.044 77.873 4 6.4725 3.2461 -1.6148 3.1483 0.5833 1.6868 0.0277 -0.7731 -1.0493 0.2804 -0.3599 -0.4653 0.3051 0.2279 0.3322 0.7987 0.1153 -0.0429 0.2816 -0.0577 0.6072 -3.572 55.465 72.247 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0.2444 0 0 0.2444 0 0.2444 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0.2444 0 0 0.2444 0 0.2444 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0.2444 0 0 0.2444 0 0.2444 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0.2444 0 0 0.2444 0 0.2444 0 0 0 9 1.6526 -0.283 -0.2558 3.5582 -1.3663 2.5124 0.1833 0.1337 0.2506 -0.4444 0.0122 -0.1662 -0.1563 0.073 -0.1955 0.426 0.0847 -0.0455 0.0872 -0.1403 0.4026 31.233 140.121 24.718 10 0.5657 0.2757 -0.1942 2.6622 0.3125 0.3906 -0.0173 -0.0145 0.0305 0.1947 0.0329 0.1842 -0.0301 -0.0103 -0.0156 0.3646 0.1471 -0.1167 0.077 -0.1038 0.2295 8.561 117.644 42.313 11 2.4848 1.4623 -2.1904 1.7026 -1.7795 3.3164 -0.0066 -0.3149 -0.1555 0.1235 -0.085 0.0425 -0.0656 0.3393 0.0916 0.374 0.148 -0.1071 0.1299 -0.0775 0.3713 21.66 80.418 31.964 12 1.0311 0.4272 -0.6556 1.6796 -0.1174 0.8285 -0.0491 0.029 0.0266 -0.0486 0.0722 -0.0763 -0.0181 0.0151 -0.0231 0.3693 0.1537 -0.1599 0.0924 -0.1347 0.3003 27.825 99.575 22.037 13 0.7939 0.6157 -0.6209 2.3047 -0.6387 1.3889 -0.2639 0.1583 -0.2965 -0.4678 0.0794 -0.1743 0.2854 -0.0908 0.1845 0.4936 0.1038 -0.0875 0.1405 -0.2378 0.4414 1.789 91.993 6.401 14 0.5912 0.2682 0.075 1.2418 0.6989 3.2616 -0.0032 0.0714 0.0123 -0.0075 0.023 0.1961 -0.0333 -0.1027 -0.0198 0.2839 0.1282 -0.1219 0.0797 -0.095 0.2976 0.609 109.091 24.16 15 0.7283 -0.1384 0.5401 1.7106 -0.1713 1.8873 0.0638 0.076 -0.0658 -0.1505 0.0233 0.0992 0.2912 -0.0181 -0.0871 0.4687 0.0856 -0.1163 0.0524 -0.1092 0.4089 -9.445 38.025 95.062 16 0.4967 0.0785 0.3864 1.516 0.5752 1.484 -0.003 -0.0198 -0.0388 -0.1422 0.0995 -0.0606 -0.2165 -0.0213 -0.0965 0.4242 0.1289 -0.0705 0.0821 -0.1257 0.3653 -7.177 83.413 91.469 17 0.4522 -0.0397 -0.4623 1.5634 0.6427 1.9345 0.145 -0.0584 0.1296 -0.1955 0.2554 -0.4824 -0.3768 0.4461 -0.4003 0.4319 0.0602 -0.0527 0.1961 -0.2531 0.545 13.662 71.609 90.633 18 0.21 -0.4518 -0.3319 1.0142 0.732 0.5332 -0.1153 -0.0176 0.0065 0.1845 0.1349 -0.0514 0.1729 0.0768 -0.0195 0.4743 0.0087 -0.0794 0.2999 -0.1118 0.4246 6.809 53.489 97.554
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 D12 - 36 2 X-RAY DIFFRACTION 2 D37 - 41 3 X-RAY DIFFRACTION 3 D42 - 46 4 X-RAY DIFFRACTION 4 D47 - 54 5 X-RAY DIFFRACTION 5 F - f 7 - 11 6 X-RAY DIFFRACTION 6 F - f 12 - 36 7 X-RAY DIFFRACTION 7 F - f 37 - 41 8 X-RAY DIFFRACTION 8 F - f 42 - 54 9 X-RAY DIFFRACTION 9 A1 - 168 10 X-RAY DIFFRACTION 10 A169 - 484 11 X-RAY DIFFRACTION 11 A485 - 564 12 X-RAY DIFFRACTION 12 A565 - 849 13 X-RAY DIFFRACTION 13 A850 - 964 14 X-RAY DIFFRACTION 14 A965 - 1166 15 X-RAY DIFFRACTION 15 C1 - 360 16 X-RAY DIFFRACTION 16 C361 - 887 17 X-RAY DIFFRACTION 17 C888 - 1166 18 X-RAY DIFFRACTION 18 D7 - 11