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 REFMAC5.5.0102精密化 HKL-2000データ削減 HKL-2000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 3BAE, 1UM5, 8FAB解像度 : 2.2→46.03 Å / Cor.coef. Fo :Fc : 0.957 / Cor.coef. Fo :Fc free : 0.922 / SU B : 19.141 / SU ML : 0.21 / TLS residual ADP flag : LIKELY RESIDUAL / Isotropic thermal model : Isotropic & TLS / 交差検証法 : THROUGHOUT / ESU R : 0.278 / ESU R Free : 0.236 / 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 0.27134 2734 5 % RANDOM Rwork 0.20923 - - - obs 0.21247 51677 92.55 % - all - 51677 - -
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 : 28.225 Å2 Baniso -1 Baniso -2 Baniso -3 1- 4.29 Å2 2.14 Å2 0 Å2 2- - 4.29 Å2 0 Å2 3- - - -6.43 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.2→46.03 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 7018 0 0 383 7401
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 7195 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.742 1.958 9802 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg7.744 5 910 X-RAY DIFFRACTION r_dihedral_angle_2_deg35.565 24.093 281 X-RAY DIFFRACTION r_dihedral_angle_3_deg19.223 15 1169 X-RAY DIFFRACTION r_dihedral_angle_4_deg17.965 15 32 X-RAY DIFFRACTION r_chiral_restr0.117 0.2 1115 X-RAY DIFFRACTION r_gen_planes_refined0.009 0.021 5392 X-RAY DIFFRACTION r_gen_planes_otherX-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_it0.664 1.5 4561 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it1.199 2 7429 X-RAY DIFFRACTION r_scbond_it2.1 3 2634 X-RAY DIFFRACTION r_scangle_it3.077 4.5 2373 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 : 2.2→2.257 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.358 154 - Rwork 0.297 2641 - obs - - 64.09 %
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 2.6152 -1.6034 -0.1767 1.9445 -0.0112 2.0786 0.0961 0.0099 0.0983 -0.1322 -0.0294 -0.1435 -0.1372 0.5704 -0.0667 0.0107 -0.0491 0.0088 0.3321 -0.0347 0.2877 -7.966 49.988 -5.518 2 0.9367 0.8863 0.8716 2.0105 0.087 12.6739 0.1684 -0.1628 0.1519 0.2003 -0.0128 -0.0449 -1.3664 2.0727 -0.1556 0.2282 -0.3836 0.082 0.6762 -0.1679 0.4299 -17.63 64.175 23.006 3 3.4053 -1.7059 -0.5857 2.4907 -0.4126 6.1922 -0.2492 -0.3134 -0.3637 0.4862 0.1769 0.1355 0.391 0.2275 0.0724 0.1468 0.0399 0.0418 0.2641 0.0231 0.361 -3.923 34.476 9.001 4 0.8054 -0.2267 -0.6992 1.6814 1.0972 7.3752 -0.0107 -0.0897 0.02 0.1832 0.0432 0.0627 0.4367 0.3299 -0.0325 0.0774 -0.0947 0.0201 0.3088 -0.0217 0.3156 -25.926 55.786 33.05 5 0.9098 -0.1125 -0.0084 4.0182 -0.2024 1.9216 -0.0403 -0.0586 -0.0763 -0.0016 0.0793 0.141 0.3919 -0.3643 -0.039 0.1825 -0.1443 -0.0162 0.1258 0.0264 0.2657 -39.261 32.328 14.342 6 1.5868 -0.8572 -0.0916 0.8361 0.7856 12.8102 0.0528 0.1792 -0.0295 -0.1843 0.1195 0.1753 1.1955 -2.2073 -0.1723 0.2335 -0.3785 -0.0905 0.6012 0.1275 0.4048 -46.526 47.228 -14.005 7 1.9331 -0.0844 -0.0367 4.8657 -0.0515 5.6411 0.1815 0.3772 -0.0438 -0.5737 -0.2229 -0.416 0.4919 0.1898 0.0414 0.2278 -0.0033 0.0507 0.1415 0.0333 0.3545 -27.824 20.621 -0.149 8 0.5849 0.0485 -0.0302 1.4626 -1.2889 7.5877 0.0709 0.1334 0.0654 -0.0443 -0.0776 -0.0143 0.5538 0.0511 0.0067 0.1941 -0.1362 -0.0194 0.2588 0.0231 0.3228 -35.484 50.498 -24.207
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 H1 - 125 2 X-RAY DIFFRACTION 2 H126 - 229 3 X-RAY DIFFRACTION 3 L1 - 113 4 X-RAY DIFFRACTION 4 L114 - 228 5 X-RAY DIFFRACTION 5 A1 - 125 6 X-RAY DIFFRACTION 6 A126 - 228 7 X-RAY DIFFRACTION 7 B1 - 113 8 X-RAY DIFFRACTION 8 B114 - 229