ソフトウェア 名称 バージョン 分類 NB REFMAC5.5.0102精密化 Show PDB_EXTRACT3.1 データ抽出 Show
精密化 構造決定の手法 : 分子置換開始モデル : PDB ENTRY 3ORW解像度 : 1.6→44.07 Å / Cor.coef. Fo :Fc : 0.963 / Cor.coef. Fo :Fc free : 0.957 / Occupancy max : 1 / Occupancy min : 0.5 / SU B : 3.104 / SU ML : 0.05 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R Free : 0.08 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.194 4942 5 % RANDOM Rwork 0.178 - - - obs 0.179 99109 95.6 % -
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 : 24.68 Å2 Baniso -1 Baniso -2 Baniso -3 1- -1.29 Å2 0 Å2 -1.02 Å2 2- - 1.1 Å2 0 Å2 3- - - -0.14 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.6→44.07 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 5089 0 4 737 5830
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_d0.007 0.022 5205 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.052 1.959 7041 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg5.433 5 644 X-RAY DIFFRACTION r_dihedral_angle_2_deg32.541 23.73 252 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.76 15 870 X-RAY DIFFRACTION r_dihedral_angle_4_deg20.547 15 38 X-RAY DIFFRACTION r_chiral_restr0.073 0.2 759 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.021 4018 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_it0.347 1.5 3203 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it0.672 2 5148 X-RAY DIFFRACTION r_scbond_it1.219 3 2002 X-RAY DIFFRACTION r_scangle_it2.111 4.5 1893 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
Refine LS restraints NCS Dom-ID : 1 / Auth asym-ID : A / Ens-ID : 1 / 数 : 2541 / Refine-ID : X-RAY DIFFRACTION
タイプ Rms dev position (Å)Weight position medium positional0.26 0.5 medium thermal0.4 2
LS精密化 シェル 解像度 : 1.6→1.64 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.259 327 - Rwork 0.223 6586 - obs - - 90.92 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 4) 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 1.0228 0.3011 0.1613 0.9137 0.2274 0.6578 -0.0023 -0.0359 0.0898 0.0275 -0.0049 0.0199 -0.0494 0.0009 0.0073 0.0607 0.0072 0.0055 0.0383 0.0035 0.0508 17.4566 -2.762 28.3792 2 0.6687 0.236 0.2194 0.9347 0.252 0.7096 0.0045 0.0783 -0.0932 -0.0222 0.0036 0.0025 0.0727 -0.0077 -0.0081 0.064 0.0046 0.0011 0.0654 -0.0248 0.0662 -4.26 -32.9431 16.5488 3 0.4973 0.2911 0.134 0.4934 0.1528 0.252 0.0014 0.0104 -0.0013 0.0044 -0.0059 0.0133 0.0051 0.0048 0.0044 0.1636 0.0203 0.0084 0.1734 0.0068 0.1501 6.1296 -17.3179 23.0256 4 2.4725 -0.6122 -1.6253 0.1521 0.4015 1.0699 0.1485 -0.1258 0.1768 -0.0562 0.0054 -0.0363 -0.0913 0.0843 -0.1539 0.3456 0.0149 -0.1761 0.0081 -0.0224 0.1192 9.718 -17.196 24.406
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 A3 - 326 2 X-RAY DIFFRACTION 2 B3 - 326 3 X-RAY DIFFRACTION 3 A329 - 737 4 X-RAY DIFFRACTION 3 B329 - 736 5 X-RAY DIFFRACTION 4 A327 - 328 6 X-RAY DIFFRACTION 4 B327 - 328