ソフトウェア 名称 バージョン 分類 NB DENZOデータ削減 Show SCALEPACKデータスケーリング Show SOLVE2.05 位相決定 Show RESOLVE2.06 位相決定 Show REFMAC精密化 Show PDB_EXTRACT3.006 データ抽出 Show HKL-2000データ収集
精密化 構造決定の手法 : 多波長異常分散 / 解像度 : 1.88→46.32 Å / Cor.coef. Fo :Fc : 0.955 / Cor.coef. Fo :Fc free : 0.922 / Occupancy max : 1 / Occupancy min : 0.2 / SU B : 8.674 / SU ML : 0.14 / TLS residual ADP flag : LIKELY RESIDUAL / Isotropic thermal model : ISOTROPIC / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : 22 group TLS refinement defined by TLS Motion Determination (TLSMD) http://skuld.bmsc.washington.edu/~tlsmd/Rfactor 反射数 %反射 Rfree 0.248 1021 5 % Rwork 0.184 - - obs 0.187 20230 67.4 % all - 20230 -
溶媒の処理 溶媒モデル : BABINET MODEL WITH MASK原子変位パラメータ Biso mean : 39.61 Å2 Baniso -1 Baniso -2 Baniso -3 1- 3.87 Å2 0 Å2 1.43 Å2 2- - -2.26 Å2 0 Å2 3- - - -1.25 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.88→46.32 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3190 0 14 283 3487
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 3294 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.063 1.966 4497 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg5.163 5 426 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.284 23.284 134 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.694 15 524 X-RAY DIFFRACTION r_dihedral_angle_4_deg14.131 15 24 X-RAY DIFFRACTION r_chiral_restr0.069 0.2 532 X-RAY DIFFRACTION r_gen_planes_refined0.003 0.02 2478 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refined0.183 0.2 1567 X-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refined0.293 0.2 2268 X-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refined0.106 0.2 252 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.156 0.2 72 X-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refined0.105 0.2 27 X-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it0.42 2 2166 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it0.738 3 3394 X-RAY DIFFRACTION r_scbond_it1.922 6 1279 X-RAY DIFFRACTION r_scangle_it3.013 10 1100 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 : 1.88→1.93 ÅRfactor 反射数 %反射 Rfree 0.476 5 - Rwork 0.364 102 - obs - - 4.81 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 22) 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 27.956 -3.2148 -2.5297 1.1615 4.7588 25.44 -0.2617 0.2487 1.9273 -0.496 0.6066 -0.3974 -1.6654 0.5893 -0.3449 -0.0662 -0.0476 0.0459 -0.0365 0.0158 -0.0715 26.573 49.306 54.035 2 13.0841 3.0847 -2.3594 34.4326 2.0945 2.574 0.3635 1.5173 -0.6255 -0.0721 -0.1941 1.0267 0.1705 -0.974 -0.1694 -0.0249 -0.0579 0.0995 0.1619 -0.1545 0.0268 19.837 35.776 51.134 3 5.2104 2.3515 -0.756 10.2991 1.7277 4.6015 0.1103 -0.178 -0.2832 0.4269 -0.3506 -0.6486 0.2877 0.024 0.2403 -0.0838 0.0012 -0.0049 -0.1093 0.0111 -0.1262 30.011 23.678 42.763 4 10.0918 -6.2701 -0.2972 21.4403 -3.9592 7.0138 0.2389 -0.2449 0.0203 0.7267 -0.2408 0.8521 0.2238 -0.4332 0.0019 -0.0312 -0.1196 0.0451 -0.0328 -0.1927 -0.1393 20.073 21.358 46.778 5 11.0162 2.8925 4.5356 8.4519 1.3377 4.9194 0.2482 -0.1998 0.1445 -0.5639 -0.2161 0.0274 0.1138 -0.2491 -0.0321 -0.073 0.0434 0.0169 -0.1155 0.0031 -0.1076 25.315 27.666 35.013 6 3.9813 0.5968 -3.1212 6.467 1.9594 7.5381 0.0399 -0.1044 -0.2579 -0.5373 0.1031 -0.6506 0.2099 0.4006 -0.143 -0.1105 -0.0148 0.0403 -0.0787 0.025 -0.043 36.217 35.662 38.072 7 2.8025 1.3409 -1.0531 4.4417 -1.5596 5.3114 -0.0983 -0.311 -0.2591 -0.3378 -0.1275 -1.0932 0.1025 0.7041 0.2257 -0.2064 -0.0125 0.0612 -0.0298 0.0408 0.0397 42.209 41.571 41.485 8 33.4764 6.7316 -6.7472 6.521 1.1607 6.5687 -0.4578 0.295 0.8097 -0.3479 0.2093 -0.3178 -0.1946 0.031 0.2485 -0.1098 -0.0817 -0.0695 -0.0529 0.0665 -0.141 34.763 50.125 43.172 9 23.9622 5.6292 -10.5 2.0185 -9.2868 71.4222 0.3154 0.2158 0.0637 0.2302 -0.2076 0.512 -0.6022 -3.0913 -0.1078 0.0179 -0.0644 -0.0395 0.2132 -0.1163 0.0684 18.565 41.582 41.028 10 1.1538 -0.651 0.3758 6.6968 -2.4001 3.8317 -0.0195 -0.2846 0.0626 0.0756 0.0288 -0.0387 -0.438 -0.0496 -0.0093 -0.1052 -0.0096 -0.0171 -0.0154 -0.0242 -0.1367 31.045 49.662 44.921 11 52.8148 12.8932 7.2098 28.7866 -3.8079 32.5075 -0.1684 0.5342 -3.0455 0.2207 1.4527 0.4391 4.0008 -0.521 -1.2843 0.1939 0.0845 0.0765 0.0463 0.215 0.1557 27.131 29.285 59.403 12 12.5667 6.4327 -4.0506 26.4256 -5.5369 12.4337 0.1938 0.1053 0.4156 0.4068 0.0425 0.0462 -0.295 0.3575 -0.2363 -0.1763 -0.018 0.0403 -0.0356 0.0157 -0.1988 29.089 46.217 8.798 13 8.562 8.4094 -2.416 8.2594 -2.3729 0.6817 0.0602 0.3779 -0.7805 -0.8866 -0.3175 -1.0874 1.0213 0.0007 0.2574 0.2065 0.0214 0.1362 -0.0042 -0.0238 0.0828 24.388 30.959 11.129 14 3.9083 -4.1686 -6.3486 17.0009 1.7347 12.3333 -0.2569 0.1292 -0.175 -0.0402 0.2447 1.0461 0.8864 -0.93 0.0122 0.047 -0.1662 -0.088 -0.0781 0.0002 -0.0783 12.003 28.49 20.317 15 18.8253 6.1572 5.5533 9.2682 1.712 15.0626 0.5525 0.1256 -0.3765 -0.4866 -0.4777 -0.3411 2.2059 0.2526 -0.0749 0.3647 -0.0015 0.1511 -0.2538 -0.0012 -0.1276 19.989 21.38 14.555 16 4.4047 -2.9154 1.0182 10.2236 -3.3034 4.0108 0.1978 0.2231 0.1082 -0.2746 -0.0813 -0.2505 0.3069 0.0031 -0.1166 -0.0133 -0.0069 -0.0271 -0.13 -0.0253 -0.1018 19.874 29.582 25.604 17 12.1982 1.1386 3.5736 9.81 0.1542 13.152 -0.1017 -0.3909 -0.4309 0.5014 0.0754 0.5954 0.391 -1.0185 0.0263 -0.0091 -0.0069 0.0576 -0.0522 -0.0493 -0.0959 10.77 41.671 27.033 18 2.8448 -1.1206 0.6874 3.0662 0.0623 1.9469 -0.0148 -0.0279 -0.2618 -0.1852 0.1088 0.1699 -0.0048 -0.211 -0.094 -0.0477 -0.0059 -0.0018 -0.0877 0.0208 -0.0719 13.598 42.435 19.013 19 3.6895 -0.766 0.7475 1.7129 -0.5082 2.5383 0.0686 0.1172 0.0999 0.1275 -0.0665 -0.0183 -0.3208 -0.1047 -0.0021 -0.0273 -0.0066 -0.0104 -0.1279 0.0163 -0.0758 16.598 52.86 20.937 20 4.436 2.4909 0.0047 1.8539 -1.5118 5.0382 -0.176 0.2181 -0.463 0.3862 -0.286 -0.2679 0.4032 0.6104 0.462 -0.0252 -0.0219 -0.0144 -0.0065 0.0142 -0.0504 27.358 46.97 22.251 21 1.8737 0.0214 1.6615 1.3178 1.021 4.504 -0.1608 0.4326 0.2337 -0.0593 0.0247 -0.0578 -0.1967 0.6145 0.1361 -0.0542 -0.0438 0.028 -0.0087 0.0354 -0.0708 25.752 52.769 16.166 22 6.1834 15.3255 14.99 46.1507 35.6134 36.6299 0.3842 1.0876 -0.6378 0.7408 2.108 -1.1876 2.5931 -0.0979 -2.4922 0.4686 0.0261 0.1126 0.3542 -0.0815 0.1123 18.767 34.069 3.23
精密化 TLSグループ 大きな表を表示 (5 x 22) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A1 - 8 2 X-RAY DIFFRACTION 2 A9 - 20 3 X-RAY DIFFRACTION 3 A21 - 41 4 X-RAY DIFFRACTION 4 A42 - 60 5 X-RAY DIFFRACTION 5 A61 - 78 6 X-RAY DIFFRACTION 6 A79 - 105 7 X-RAY DIFFRACTION 7 A106 - 136 8 X-RAY DIFFRACTION 8 A137 - 148 9 X-RAY DIFFRACTION 9 A149 - 156 10 X-RAY DIFFRACTION 10 A157 - 204 11 X-RAY DIFFRACTION 11 A205 - 209 12 X-RAY DIFFRACTION 12 B1 - 13 13 X-RAY DIFFRACTION 13 B14 - 25 14 X-RAY DIFFRACTION 14 B26 - 40 15 X-RAY DIFFRACTION 15 B41 - 58 16 X-RAY DIFFRACTION 16 B59 - 78 17 X-RAY DIFFRACTION 17 B79 - 91 18 X-RAY DIFFRACTION 18 B92 - 112 19 X-RAY DIFFRACTION 19 B113 - 149 20 X-RAY DIFFRACTION 20 B150 - 169 21 X-RAY DIFFRACTION 21 B170 - 202 22 X-RAY DIFFRACTION 22 B203 - 209