ソフトウェア 名称 バージョン 分類 NB SCALAデータスケーリング Show REFMAC精密化 Show PDB_EXTRACT2 データ抽出 Show MOSFLMデータ削減 MOLREP位相決定
精密化 構造決定の手法 : 分子置換開始モデル : PDB entry 2QF4解像度 : 2.23→23.83 Å / Cor.coef. Fo :Fc : 0.945 / Cor.coef. Fo :Fc free : 0.886 / SU B : 11.789 / SU ML : 0.158 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / σ(I) : 0 / ESU R : 0.313 / ESU R Free : 0.253 / 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 0.268 365 4.6 % RANDOM Rwork 0.194 - - - obs 0.197 7870 92.72 % -
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 : 20.21 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.9 Å2 0 Å2 -1.19 Å2 2- - -1.76 Å2 0 Å2 3- - - -2.16 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.23→23.83 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 1161 0 0 74 1235
拘束条件 大きな表を表示 (5 x 24) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.012 0.022 1170 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 734 X-RAY DIFFRACTION r_angle_refined_deg1.376 1.957 1587 X-RAY DIFFRACTION r_angle_other_deg0.882 3 1831 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.329 5 156 X-RAY DIFFRACTION r_dihedral_angle_2_deg38.843 27.111 45 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.396 15 208 X-RAY DIFFRACTION r_dihedral_angle_4_deg22.352 15 3 X-RAY DIFFRACTION r_chiral_restr0.075 0.2 201 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.02 1304 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 190 X-RAY DIFFRACTION r_nbd_refined0.195 0.2 170 X-RAY DIFFRACTION r_nbd_other0.19 0.2 773 X-RAY DIFFRACTION r_nbtor_refined0.163 0.2 536 X-RAY DIFFRACTION r_nbtor_other0.086 0.2 684 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.155 0.2 67 X-RAY DIFFRACTION r_symmetry_vdw_refined0.145 0.2 13 X-RAY DIFFRACTION r_symmetry_vdw_other0.254 0.2 18 X-RAY DIFFRACTION r_symmetry_hbond_refined0.195 0.2 10 X-RAY DIFFRACTION r_mcbond_it0.688 1.5 1001 X-RAY DIFFRACTION r_mcbond_other0.124 1.5 327 X-RAY DIFFRACTION r_mcangle_it0.867 2 1257 X-RAY DIFFRACTION r_scbond_it1.541 3 431 X-RAY DIFFRACTION r_scangle_it2.393 4.5 330
LS精密化 シェル 解像度 : 2.23→2.29 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.225 24 - Rwork 0.226 536 - obs - 560 91.21 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 7) 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 23.2698 -8.7235 27.7671 23.6101 -17.6032 52.0674 0.4178 0.7015 -0.7978 -0.3398 0.0462 1.3097 0.2266 -1.0167 -0.464 -0.0477 -0.0079 0.1396 0.1195 -0.0302 0.0384 -2.9988 0.5315 21.2704 2 3.6536 -2.297 0.5862 6.6563 -0.4888 6.3579 0.143 0.4013 -0.0198 -0.1976 -0.1348 -0.5321 0.2105 0.582 -0.0082 -0.04 0.017 -0.0578 -0.0972 0.0044 -0.0575 13.8816 -11.1727 21.2351 3 6.849 2.9712 -7.003 9.4749 -15.6268 36.3135 -0.2493 0.1338 -0.5355 -0.4555 0.7656 0.7835 0.8116 -1.0738 -0.5163 -0.153 0.0215 -0.0027 0.077 0.0259 0.079 -2.7817 -9.2103 21.4098 4 1.3404 -0.0522 -1.1022 2.2309 2.0035 3.182 0.1052 -0.0585 -0.2041 0.0318 0.0617 -0.1284 0.003 -0.0918 -0.1669 -0.0135 0.0147 -0.0579 -0.0633 0.0426 -0.0569 6.6279 -4.1757 17.3073 5 0.3114 -0.6048 0.981 2.5516 -0.5141 4.4959 -0.0666 0.2348 -0.2909 -0.0869 0.0373 -0.2355 0.4105 -0.1283 0.0292 -0.0408 0.0143 0.0169 -0.0494 -0.0398 -0.0243 10.098 -9.0972 15.3559 6 3.6648 0.2314 1.0859 2.5071 -0.9668 3.7835 -0.0853 0.3545 0.0151 -0.471 0.1056 -0.1378 -0.0796 0.2958 -0.0203 -0.0238 -0.0377 0.049 -0.0712 -0.0174 -0.1301 11.3757 5.0659 3.5417 7 11.6022 0.1511 7.3899 5.8571 -1.6869 10.3829 0.0198 -0.1878 -0.2321 0.1715 0.0671 -0.2151 -0.0709 -0.0852 -0.087 -0.0023 0.0156 -0.0235 -0.1825 -0.0226 -0.0946 9.2215 -0.0255 21.1263
精密化 TLSグループ ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA110 - 115 5 - 10 2 X-RAY DIFFRACTION 2 AA116 - 135 11 - 30 3 X-RAY DIFFRACTION 3 AA136 - 143 31 - 38 4 X-RAY DIFFRACTION 4 AA144 - 160 39 - 55 5 X-RAY DIFFRACTION 5 AA161 - 174 56 - 69 6 X-RAY DIFFRACTION 6 AA175 - 258 70 - 153 7 X-RAY DIFFRACTION 7 AA259 - 272 154 - 167