ソフトウェア 名称 バージョン 分類 StructureStudio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 : PDB ENTRY 3lGJ解像度 : 2.1→46.88 Å / Cor.coef. Fo :Fc : 0.942 / Cor.coef. Fo :Fc free : 0.913 / SU B : 10.621 / SU ML : 0.124 / Isotropic thermal model : isotropic, TLS / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R Free : 0.183 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN ADDED IN THERfactor 反射数 %反射 Selection details Rfree 0.256 972 5.2 % RANDOM Rwork 0.21 - - - all 0.212 18898 - - obs 0.212 18828 98.4 % -
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 : 25.14 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.14 Å2 -0.07 Å2 0 Å2 2- - -0.14 Å2 0 Å2 3- - - 0.21 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.1→46.88 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 1804 0 6 134 1944
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_d0.016 0.022 1871 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 1296 X-RAY DIFFRACTION r_angle_refined_deg1.596 1.942 2531 X-RAY DIFFRACTION r_angle_other_deg0.859 3 3149 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.164 5 232 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.649 24.563 103 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.716 15 357 X-RAY DIFFRACTION r_dihedral_angle_4_deg22.153 15 19 X-RAY DIFFRACTION r_chiral_restr0.103 0.2 280 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 2093 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 376 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_it0.838 1.5 1116 X-RAY DIFFRACTION r_mcbond_other0.176 1.5 464 X-RAY DIFFRACTION r_mcangle_it1.639 2 1799 X-RAY DIFFRACTION r_scbond_it2.578 3 755 X-RAY DIFFRACTION r_scangle_it4.387 4.5 726 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 : 2.1→2.15 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.277 61 - Rwork 0.316 1265 - obs - - 95.6 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 8) 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 3.0277 0.5248 -0.4235 1.2994 0.0977 0.7544 -0.045 0.0793 -0.1692 -0.1256 0.0558 -0.1509 -0.003 0.0356 -0.0108 0.064 -0.0277 0.0229 0.1098 -0.0224 0.0643 -9.2799 44.5711 12.9969 2 26.406 13.7781 5.6925 10.6479 8.2406 9.2594 -0.2263 0.8256 -0.1643 -0.3992 -0.0569 0.1564 -0.4816 -0.5196 0.2832 0.2645 -0.1179 -0.1519 0.3066 -0.1152 0.3527 -28.2977 30.9548 3.1081 3 2.3149 0.4005 -0.5514 0.7509 -0.4754 1.1501 -0.0434 0.0991 -0.0854 -0.0659 0.0503 -0.0745 0.0144 0.0136 -0.0069 0.065 -0.021 0.0182 0.1078 -0.0388 0.0731 -10.286 44.673 10.3882 4 2.2228 0.6192 -0.8321 1.3594 -0.6492 2.0885 0.0381 0.0277 -0.0217 0.0726 -0.019 -0.1538 -0.1903 0.1344 -0.0192 0.047 -0.0062 -0.0059 0.1038 -0.0257 0.067 -12.6233 47.3807 14.5618 5 2.3755 0.6091 0.4497 0.967 0.5004 1.2228 -0.2241 0.4093 0.2075 -0.1168 0.0859 0.1476 -0.1303 -0.1334 0.1383 0.0584 -0.0509 -0.0323 0.2045 0.0423 0.0871 -33.072 50.5876 4.8916 6 19.9634 6.3866 7.3322 2.6732 2.1724 2.7439 0.0478 -0.1038 0.1286 0.0427 -0.0627 0.1066 -0.0026 -0.0059 0.0149 0.1591 -0.1016 0.017 0.2356 -0.0379 0.0863 -10.1526 63.598 19.0348 7 2.6215 0.3522 -0.3969 1.6824 0.9842 1.5225 -0.1426 0.4485 0.1457 -0.1875 0.0035 0.2243 -0.1206 -0.1051 0.1391 0.0574 -0.0091 -0.0501 0.179 0.0531 0.0674 -30.3952 50.6246 4.1446 8 3.2332 -0.388 -0.7942 1.5979 1.229 2.1997 -0.1029 0.4361 0.0405 -0.1054 -0.0549 0.2526 -0.0245 -0.2505 0.1578 0.0153 -0.018 -0.0314 0.1375 0.0023 0.094 -31.1453 46.6689 7.3503
精密化 TLSグループ ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A2 - 36 2 X-RAY DIFFRACTION 2 A37 - 52 3 X-RAY DIFFRACTION 3 A53 - 96 4 X-RAY DIFFRACTION 4 A97 - 115 5 X-RAY DIFFRACTION 5 B2 - 35 6 X-RAY DIFFRACTION 6 B36 - 51 7 X-RAY DIFFRACTION 7 B52 - 96 8 X-RAY DIFFRACTION 8 B97 - 115