ソフトウェア 名称 バージョン 分類 MsDCデータ収集 PHENIXモデル構築 REFMAC5.5.0109精密化 HKL-2000データ削減 HKL-2000データスケーリング PHENIX位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 1.55→47.78 Å / Cor.coef. Fo :Fc : 0.969 / Cor.coef. Fo :Fc free : 0.958 / SU B : 3.034 / SU ML : 0.05 / 交差検証法 : THROUGHOUT / ESU R : 0.079 / 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 POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.20223 1851 5 % RANDOM Rwork 0.1747 - - - obs 0.17615 35030 93.19 % - all - 36885 - -
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 : 27.642 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.03 Å2 0 Å2 -0.02 Å2 2- - -0.01 Å2 0 Å2 3- - - 0.02 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.55→47.78 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 1818 0 0 253 2071
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_d0.027 0.022 1870 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg2.307 1.962 2542 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg6.512 5 220 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.732 23.404 94 X-RAY DIFFRACTION r_dihedral_angle_3_deg16.519 15 334 X-RAY DIFFRACTION r_dihedral_angle_4_deg20.375 15 20 X-RAY DIFFRACTION r_chiral_restr0.182 0.2 284 X-RAY DIFFRACTION r_gen_planes_refined0.013 0.021 1415 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_it1.41 1.5 1111 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it2.472 2 1800 X-RAY DIFFRACTION r_scbond_it4.02 3 759 X-RAY DIFFRACTION r_scangle_it6.61 4.5 742 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 : 1.55→1.59 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.406 83 - Rwork 0.342 1540 - obs - - 55.83 %
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 3.343 -0.947 0.8911 1.3955 -0.4607 1.8827 -0.0007 0.2829 -0.1584 -0.164 -0.0016 -0.0584 0.2036 -0.0078 0.0023 0.1036 -0.0114 0.021 0.0964 -0.0135 0.0294 21.9531 -8.2065 -4.5674 2 1.9939 -0.5241 0.8679 0.9418 -0.2439 1.1959 -0.058 -0.1563 -0.0277 0.0137 0.057 0.0192 0.1234 -0.2031 0.0009 0.0645 -0.015 0.008 0.1011 -0.0011 0.0524 16.8816 -3.7789 7.5315 3 5.1408 -1.3682 0.0207 2.2701 0.3629 1.8645 0.08 0.2318 -0.3478 -0.2087 -0.1072 0.2252 0.1516 -0.2634 0.0272 0.0628 -0.0355 -0.0172 0.1262 -0.0182 0.0565 10.4694 -4.6171 -3.9313 4 2.6869 -0.2197 0.8207 1.5192 -0.2637 1.1023 0.0045 0.2202 0.049 -0.0879 -0.0042 0.1019 0.064 -0.199 -0.0003 0.0333 -0.018 -0.0004 0.1315 0.0002 0.0518 10.3298 -0.8959 -5.3375 5 0.4402 -0.0303 0.1813 1.522 0.5347 0.8831 -0.0004 0.0102 0.0165 -0.0198 0.0357 -0.0954 -0.0194 0.0388 -0.0353 0.0734 -0.002 0.0072 0.0473 0.0021 0.0722 27.1718 6.1746 21.3149 6 6.2547 4.4125 -5.15 3.2931 -4.8785 12.9832 -0.119 0.4007 1.0055 -0.0979 0.3897 0.6422 -0.0319 -0.7099 -0.2707 0.1005 -0.069 -0.0008 0.1311 0.0733 0.2772 24.0525 10.4242 -5.6004 7 1.475 0.0989 2.4385 0.3442 1.0565 6.5165 -0.1331 0.1959 0.2188 0.0276 0.1054 -0.1441 -0.0457 0.5255 0.0277 0.0709 -0.0276 0.0211 0.1132 0.0032 0.1942 33.2678 -1.204 3.0357
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 A343 - 377 2 X-RAY DIFFRACTION 2 A378 - 404 3 X-RAY DIFFRACTION 3 A405 - 425 4 X-RAY DIFFRACTION 4 A426 - 453 5 X-RAY DIFFRACTION 5 A454 - 531 6 X-RAY DIFFRACTION 6 A532 - 550 7 X-RAY DIFFRACTION 7 A551 - 570