ソフトウェア 名称 バージョン 分類 SBC-Collectデータ収集 MOLREP位相決定 REFMAC5.5.0054精密化 HKL-3000データ削減 HKL-3000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 2NZH解像度 : 1.5→34.82 Å / Cor.coef. Fo :Fc : 0.966 / Cor.coef. Fo :Fc free : 0.948 / SU B : 2.854 / SU ML : 0.049 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 2 / σ(I) : 2 / ESU R : 0.075 / ESU R Free : 0.078 / 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 0.20057 1628 5.1 % RANDOM Rwork 0.16564 - - - all 0.169 32171 - - obs 0.16744 30543 98.51 % -
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 : 8.352 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.59 Å2 0 Å2 0 Å2 2- - 1.38 Å2 0 Å2 3- - - -0.79 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.5→34.82 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 1653 0 21 256 1930
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_d0.02 0.022 1734 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 1183 X-RAY DIFFRACTION r_angle_refined_deg1.745 1.995 2351 X-RAY DIFFRACTION r_angle_other_deg0.915 3 2918 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.495 5 224 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.832 25.455 77 X-RAY DIFFRACTION r_dihedral_angle_3_deg12.825 15 304 X-RAY DIFFRACTION r_dihedral_angle_4_deg25.494 15 9 X-RAY DIFFRACTION r_chiral_restr0.106 0.2 270 X-RAY DIFFRACTION r_gen_planes_refined0.009 0.021 1914 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 315 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_it1.093 1.5 1088 X-RAY DIFFRACTION r_mcbond_other0.344 1.5 438 X-RAY DIFFRACTION r_mcangle_it1.781 2 1765 X-RAY DIFFRACTION r_scbond_it2.858 3 646 X-RAY DIFFRACTION r_scangle_it4.593 4.5 580 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 : 1.5→1.538 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.277 87 - Rwork 0.255 1913 - obs - - 84.85 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 20) 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 6.7219 -3.3938 -3.2031 7.9324 1.8557 10.0913 -0.0107 0.0081 -0.0632 -0.108 0.0121 -0.0289 0.2035 0.062 -0.0013 0.0723 -0.0151 -0.0111 0.0382 0.0143 0.0347 3.172 13.5612 -6.4994 2 0.9482 0.4066 0.2518 3.8991 0.8914 0.8122 -0.0003 -0.0539 0.0595 0.1609 0.025 0.1384 0.0546 -0.0538 -0.0247 0.0712 0.0058 -0.0031 0.0573 -0.0023 0.0293 3.5318 33.2036 3.6137 3 4.3554 -3.4184 -0.3361 2.8017 0.6316 1.2359 -0.0249 0.0471 0.2605 0.0085 0.057 -0.2346 -0.0938 0.2357 -0.0322 0.0727 -0.0065 -0.0233 0.1362 -0.0284 0.1226 20.3061 41.7996 2.7607 4 2.0606 0.107 0.3639 0.3965 -0.0457 0.9343 -0.0376 0.0519 0.0725 0.059 0.0549 -0.0317 0.0596 -0.0227 -0.0174 0.0732 0.0183 -0.0071 0.0413 -0.0218 0.0536 11.6128 37.444 4.67 5 1.2229 0.0884 -0.2041 0.7295 -0.2704 1.4905 -0.062 0.0132 0.0758 -0.0018 0.0051 -0.0949 0.0204 0.0209 0.0569 0.0802 0.004 -0.0174 0.0645 -0.0177 0.059 11.1789 38.6711 0.5152 6 10.7344 4.0707 3.1024 4.0201 2.0276 9.678 -0.2313 0.6076 0.7093 -0.3328 0.1901 0.2131 -0.5949 0.2594 0.0413 0.1089 -0.0089 -0.0275 0.0618 0.0361 0.0909 5.7194 46.4417 -1.1075 7 2.0232 -1.431 0.8647 3.3774 -1.0329 1.1821 0.0236 -0.0652 0.0395 0.0821 -0.022 -0.282 0.1018 0.0259 -0.0016 0.0732 0.0116 -0.02 0.0615 -0.0074 0.0668 7.7528 27.8806 2.9171 8 1.7034 0.4379 1.4519 0.7021 -0.9816 5.3114 0.0665 -0.0009 -0.1334 0.0054 -0.0063 -0.1138 0.1208 0.1384 -0.0602 0.0706 0.0294 -0.0015 0.0625 -0.0116 0.0809 15.183 30.9714 5.8967 9 6.458 -0.718 -0.8254 0.5496 -0.1033 1.8241 0.0422 0.1719 0.1421 -0.0473 -0.015 -0.0582 -0.0318 0.0854 -0.0272 0.0578 -0.0032 0.0017 0.0469 -0.0052 0.0562 6.8085 35.8674 -9.504 10 1.4101 0.328 -0.3002 4.1948 1.8195 7.5068 -0.0139 -0.0257 0.0713 0.128 0.0559 0.0833 0.345 -0.1415 -0.0419 0.0336 -0.0075 0.0003 0.0786 0.0123 0.0412 -4.67 30.0338 0.9162 11 5.787 0.7444 3.5147 7.16 3.0152 13.3759 -0.0168 -0.3234 0.0686 0.3048 0.1409 -0.0253 -0.2907 -0.2793 -0.1241 0.1028 0.0274 0.0268 0.0841 0.0099 0.082 9.081 49.3954 38.0617 12 1.2522 -0.2523 -0.483 2.1864 0.8584 2.1363 -0.012 0.0929 -0.1506 -0.0187 -0.1029 0.0829 -0.0954 0.0569 0.1149 0.0553 -0.0007 -0.0183 0.0729 0.005 0.0319 19.0397 42.3774 20.5787 13 4.1727 -0.1935 2.2991 1.2749 0.4689 3.1287 -0.0581 0.323 0.0833 0.0166 0.019 -0.1826 -0.1938 0.4074 0.0391 0.0814 -0.0274 -0.0071 0.1066 0.0144 0.0731 27.3324 43.4208 16.6866 14 6.4321 3.1082 2.4513 3.402 0.6129 3.7434 -0.1347 0.041 0.4343 -0.225 -0.04 0.1531 -0.0813 0.0167 0.1747 0.0888 0.0219 -0.0135 0.0457 -0.005 0.0579 18.4857 45.6678 15.0137 15 3.3946 -1.2145 -1.0141 0.4675 0.0009 6.6491 -0.0998 0.0866 0.0455 0.046 -0.0668 -0.0534 -0.1057 0.3634 0.1665 0.0475 -0.003 -0.0109 0.1205 0.0074 0.0763 33.2422 37.9197 24.8814 16 0.9261 -1.0174 -0.5287 2.5035 1.1331 2.0894 0.0445 -0.0049 0.0885 0.0385 0.0154 -0.1823 -0.0015 0.1692 -0.0599 0.0454 -0.0086 -0.0072 0.0713 -0.0077 0.0614 21.8124 41.4501 21.0057 17 10.278 2.2946 -0.3846 7.3067 3.0946 5.4758 0.2509 -0.1195 0.6855 -0.0156 0.0693 -0.3221 -0.4712 0.2892 -0.3201 0.1203 -0.0492 0.019 0.0444 0.0166 0.1311 27.4021 52.7425 17.9016 18 2.4883 0.5011 2.2082 0.9621 -1.3994 5.9343 0.0816 -0.121 0.0489 0.1063 -0.0303 0.0502 -0.1382 -0.0281 -0.0513 0.0892 -0.0085 -0.0089 0.1177 -0.0306 0.063 25.826 41.9295 30.4623 19 6.9319 3.1101 3.6682 2.9055 2.0288 3.6993 0.0861 -0.0443 -0.2705 -0.0101 -0.0219 -0.042 0.0511 0.0563 -0.0643 0.05 0.0043 -0.0025 0.0364 -0.0063 0.0477 22.3191 33.6826 27.4022 20 0.8394 -0.7404 -0.3447 3.0541 0.1469 8.2223 0.021 -0.0354 -0.0674 0.1014 -0.0499 0.0658 -0.2477 -0.2027 0.0289 0.0439 -0.0108 -0.0088 0.0728 -0.0056 0.0574 10.3445 37.6501 21.8711
精密化 TLSグループ 大きな表を表示 (5 x 20) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A0 - 8 2 X-RAY DIFFRACTION 2 A9 - 20 3 X-RAY DIFFRACTION 3 A21 - 26 4 X-RAY DIFFRACTION 4 A27 - 39 5 X-RAY DIFFRACTION 5 A40 - 55 6 X-RAY DIFFRACTION 6 A56 - 61 7 X-RAY DIFFRACTION 7 A62 - 72 8 X-RAY DIFFRACTION 8 A73 - 84 9 X-RAY DIFFRACTION 9 A85 - 101 10 X-RAY DIFFRACTION 10 A102 - 109 11 X-RAY DIFFRACTION 11 B0 - 7 12 X-RAY DIFFRACTION 12 B8 - 22 13 X-RAY DIFFRACTION 13 B23 - 38 14 X-RAY DIFFRACTION 14 B39 - 46 15 X-RAY DIFFRACTION 15 B47 - 55 16 X-RAY DIFFRACTION 16 B56 - 71 17 X-RAY DIFFRACTION 17 B72 - 80 18 X-RAY DIFFRACTION 18 B81 - 89 19 X-RAY DIFFRACTION 19 B90 - 101 20 X-RAY DIFFRACTION 20 B102 - 109