ソフトウェア 名称 バージョン 分類 SBC-Collectデータ収集 HKL-3000位相決定 SHELXモデル構築 MLPHARE位相決定 Cootモデル構築 ARP/wARPモデル構築 REFMAC5.5.0102精密化 HKL-3000データ削減 HKL-3000データスケーリング SHELX位相決定
精密化 構造決定の手法 : 多波長異常分散 / 解像度 : 1.85→40 Å / Cor.coef. Fo :Fc : 0.961 / Cor.coef. Fo :Fc free : 0.929 / SU B : 7.157 / SU ML : 0.096 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 2 / σ(I) : 2 / ESU R : 0.135 / ESU R Free : 0.137 / 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 0.21994 4915 5 % RANDOM Rwork 0.16347 - - - all 0.168 98246 - - obs 0.16633 93331 99.26 % -
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 : 9.062 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.69 Å2 0 Å2 0.12 Å2 2- - -1.06 Å2 0 Å2 3- - - -0.63 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.85→40 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8548 0 9 1525 10082
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_d0.019 0.022 8801 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 5949 X-RAY DIFFRACTION r_angle_refined_deg1.623 1.952 11967 X-RAY DIFFRACTION r_angle_other_deg0.991 3 14421 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.476 5 1115 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.005 23.864 427 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.748 15 1414 X-RAY DIFFRACTION r_dihedral_angle_4_deg17.101 15 72 X-RAY DIFFRACTION r_chiral_restr0.101 0.2 1291 X-RAY DIFFRACTION r_gen_planes_refined0.008 0.021 10023 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 1825 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_it0.902 1.5 5494 X-RAY DIFFRACTION r_mcbond_other0.303 1.5 2247 X-RAY DIFFRACTION r_mcangle_it1.509 2 8759 X-RAY DIFFRACTION r_scbond_it2.846 3 3307 X-RAY DIFFRACTION r_scangle_it4.272 4.5 3200 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 : 1.849→1.897 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.343 397 - Rwork 0.282 6714 - obs - - 97.44 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 40) 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 1.8545 1.94 0.3828 4.0171 3.8506 6.3758 0.4024 -0.3324 -0.3353 0.3843 -0.3868 -0.2386 0.4254 -0.1403 -0.0157 0.2575 -0.0171 -0.0819 0.0588 0.0657 0.2398 16.4887 -5.7725 56.1463 2 20.5187 2.8592 -4.5774 -2.2628 -0.6754 -1.7629 -0.4333 0.7144 0.3678 -0.0079 0.407 -0.1433 0.2161 -0.3144 0.0263 0.4083 -0.1293 0.1423 0.2638 -0.0833 0.1963 7.4129 -0.453 64.7718 3 6.9514 0.2207 -4.2337 -0.6247 0.0772 2.8115 -0.1809 -0.054 -0.5272 0.0309 -0.1159 -0.0516 0.2041 -0.0187 0.2968 0.1443 0.0184 0.0425 0.0589 0.0303 0.2753 17.8824 7.4529 67.5413 4 2.7406 3.7927 2.4141 4.3451 4.4842 7.3228 -0.1884 0.1707 -0.6426 -0.1362 0.3962 -0.6789 0.266 0.9871 -0.2078 0.2128 0.128 0.0194 0.1559 -0.0428 0.4561 25.5287 -4.3435 48.6136 5 1.1751 1.7091 0.6023 2.7196 1.488 1.6595 0.0014 0.0328 -0.2665 -0.0084 0.1166 -0.4046 0.0836 0.1543 -0.118 0.0567 0.0286 0.0093 0.0423 0.0135 0.1772 21.5164 6.1035 48.3691 6 0.8957 0.6874 -0.8849 1.4896 -1.3459 1.2709 -0.0764 0.0681 -0.1215 -0.0624 0.012 -0.0793 0.0796 -0.0616 0.0644 0.1077 -0.0267 0.0135 0.0682 -0.0105 0.0899 6.3844 11.2589 70.4058 7 1.5074 -0.1448 -0.4615 1.8837 -0.491 0.9872 -0.0178 -0.0145 -0.0147 0.1371 -0.095 -0.1352 -0.0759 0.0809 0.1128 0.0779 -0.0206 -0.0068 0.0594 -0.0012 0.0735 16.9243 25.7388 64.6166 8 2.8936 2.4453 -1.3442 2.2252 -1.5227 1.2855 0.1523 -0.0535 0.1539 0.1961 -0.0206 0.1579 -0.1504 -0.0151 -0.1317 0.1354 -0.0078 0.041 0.0526 -0.0057 0.0585 2.4163 16.8478 79.0468 9 2.9786 0.4626 2.9417 3.4287 -2.5624 17.9104 -0.1101 -0.0471 0.0071 0.0338 -0.2589 -0.3604 -0.6403 0.2453 0.369 0.0475 -0.0293 0.0053 0.0402 -0.0069 0.1196 19.8233 33.0078 62.9792 10 1.2011 0.5889 -0.2962 1.6448 -0.0474 1.2334 -0.009 0.0094 -0.0994 -0.0392 0.0007 -0.2572 0.0701 0.1016 0.0083 0.0723 0.0256 0.0089 0.0643 0.0123 0.0891 18.288 20.0741 45.998 11 2.3973 0.172 0.0168 0.6821 -0.1104 0.3831 -0.0894 0.0782 0.1411 -0.122 0.0591 -0.0538 0.0362 -0.0042 0.0303 0.0924 0.0005 0.0085 0.0723 0.0268 0.051 6.6569 24.0531 32.826 12 1.9803 -0.1451 0.4585 2.4142 -1.3334 4.5486 0.0617 0.0375 0.1151 0.1486 0.1006 0.1563 -0.2111 -0.2241 -0.1623 0.0693 0.0434 -0.0259 0.0653 0.0499 0.1145 -17.6626 28.6308 34.9317 13 1.381 -0.6335 -0.3412 1.9825 0.2766 0.4791 0.0159 -0.0052 -0.0502 -0.0698 -0.0214 0.2147 -0.0511 -0.0356 0.0056 0.0927 -0.0252 -0.0072 0.0781 0.0037 0.0474 -15.3192 3.574 42.9828 14 2.6237 -1.0478 0.1811 1.2113 -1.2487 0.8842 -0.0973 -0.2542 0.2113 0.3958 0.0661 -0.1252 -0.3074 0.0101 0.0312 0.1921 -0.0179 0.0001 0.1078 -0.025 0.0538 -7.7444 5.0794 54.6047 15 5.6908 -5.8084 0.1383 8.5047 1.4359 0.8338 -0.2471 -0.2959 0.1172 0.5819 0.1808 0.1037 0.1354 -0.0654 0.0662 0.1635 -0.002 0.0585 0.1231 -0.0146 0.0561 -12.421 9.1593 54.5888 16 0.5277 0.2657 -0.2534 0.6933 -0.496 0.4019 -0.0263 0.0348 0.0145 -0.03 0.0442 0.0584 0.0112 -0.0442 -0.0178 0.0894 -0.0074 -0.013 0.0922 0.003 0.0549 -8.0526 7.6 45.0952 17 5.0586 2.5259 -0.0841 7.201 -0.3563 3.809 0.0538 -0.0956 -0.2928 0.5352 -0.0655 -0.18 0.0054 -0.2034 0.0118 0.0616 0.0086 0.0071 0.0647 0.0314 0.0629 10.0107 -3.2765 50.3358 18 0.8544 0.5642 0.0492 0.9772 -0.2035 0.451 0.0134 0.0598 0.1313 -0.1004 0.0045 0.0328 0.0143 -0.0384 -0.0179 0.0729 0.0025 -0.0008 0.0667 0.0134 0.0555 1.3541 22.5263 38.3709 19 1.9089 0.6868 0.1991 3.9118 -1.6986 9.0232 0.0415 -0.0512 0.1795 0.0651 -0.0577 0.3438 0.071 -0.4163 0.0163 0.0365 -0.0056 0.0237 0.0497 -0.0325 0.1056 -0.3695 30.782 48.9209 20 0.8242 0.6841 0.2161 2.1813 0.2268 0.2891 -0.0689 0.0983 -0.0631 -0.3675 0.036 -0.2187 0.0249 0.005 0.0329 0.1316 -0.0053 0.0547 0.0604 -0.0047 0.0396 7.3842 7.4411 35.838 21 4.0686 -0.7477 1.6708 0.417 -1.0813 2.7882 -0.0925 0.1179 0.1384 0.1168 -0.1786 -0.2256 -0.2777 0.2604 0.2711 0.1161 0.0024 -0.0477 0.1118 0.0415 0.1487 20.032 54.8422 12.491 22 3.3524 -0.3886 -0.9776 -0.1483 0.1211 0.8483 -0.0099 0.2247 0.2958 0.0224 0.0045 -0.0474 -0.0938 -0.1182 0.0054 0.1039 0.0193 -0.0006 0.0797 0.0129 0.1585 27.3447 44.6178 19.646 23 0.4897 -0.1201 0.2667 0.4051 -0.1907 0.3943 -0.0446 -0.0632 0.0338 0.0351 0.0015 -0.0182 -0.0925 -0.0792 0.043 0.0924 0.0322 -0.0087 0.092 -0.0104 0.0377 11.6023 44.5496 13.1297 24 3.358 2.0784 -0.9544 1.7231 -0.3135 0.6174 -0.0381 0.0601 0.093 -0.0307 0.0766 -0.0083 -0.0274 -0.0127 -0.0386 0.0503 0.0014 -0.0113 0.0609 0.0224 0.0862 35.4657 38.6792 16.7956 25 0.1734 0.0874 0.0488 1.3422 0.529 0.8896 -0.0441 0.0061 -0.0989 0.0039 0.1046 -0.2401 0.0862 0.0375 -0.0605 0.0778 0.0179 -0.0039 0.0789 0.0028 0.1074 32.2795 25.1283 13.5265 26 3.8196 2.9497 -0.728 3.3654 -0.5213 1.2611 0.0293 0.1439 -0.3115 0.1223 0.0601 -0.4378 -0.0109 0.141 -0.0894 0.0225 0.033 -0.0225 0.1048 -0.016 0.1205 45.0108 34.9628 17.4625 27 0.9378 -1.3746 1.5267 1.8628 -1.4557 2.8547 0.0201 -0.0876 -0.1257 -0.0128 0.0817 0.0805 0.0932 -0.1289 -0.1018 0.1069 -0.0057 0.0291 0.0977 0.0224 0.0859 18.9939 18.7347 16.9863 28 0.697 0.7144 0.9807 1.8711 0.3573 1.7971 -0.0496 -0.0156 0.0189 0.1084 0.0334 0.1628 -0.021 -0.1043 0.0162 0.0878 -0.0006 0.0179 0.0963 -0.0055 0.0704 6.2136 30.6493 2.6603 29 2.2572 0.2498 -2.6604 1.9928 -0.3785 5.6707 -0.0691 0.1478 -0.0837 -0.144 0.0316 0.1469 0.3874 -0.3476 0.0374 0.0891 -0.057 -0.0253 0.1067 -0.0226 0.0301 9.8973 23.8721 -19.0613 30 5.1989 0.0827 1.0886 3.1338 1.0703 4.1893 0.0604 0.3732 -0.2716 -0.0552 0.1676 -0.3553 0.1616 0.2525 -0.2281 0.118 -0.0217 0.024 0.0956 -0.0775 0.0644 23.3552 21.4418 -27.6954 31 2.8118 -1.0447 -0.7737 2.6611 0.3956 1.0488 0.0097 0.1124 -0.0707 -0.1599 -0.0125 -0.2121 -0.0808 0.0602 0.0028 0.0493 -0.0236 -0.009 0.0832 0.027 0.0521 26.4955 47.2313 -20.6487 32 1.1867 0.8081 -0.2123 2.8084 1.9912 1.8208 0.1275 -0.1908 -0.2162 0.2581 0.0416 -0.4003 0.107 0.1857 -0.1691 0.0653 -0.0165 -0.0484 0.1006 0.038 0.1399 31.2451 48.2283 -8.2231 33 5.7822 -3.5155 -2.2832 5.1647 5.3771 4.8057 -0.2858 0.1578 -0.4227 0.4256 0.2771 -0.0102 0.3946 0.3675 0.0086 0.1253 0.0307 -0.0207 0.1197 0.024 0.2923 36.6561 35.5292 -14.7786 34 0.6065 0.0437 -0.0048 2.0439 1.0705 0.625 -0.0313 0.0772 0.0338 -0.1198 0.0818 -0.0823 -0.0487 0.0923 -0.0505 0.092 -0.0099 -0.007 0.1015 0.0081 0.0502 22.2468 44.0581 -13.0169 35 1.1536 0.7588 -0.907 6.5073 1.845 4.987 0.034 -0.0748 -0.0281 0.1975 0.0668 -0.3898 0.0443 0.2958 -0.1008 0.0255 0.019 -0.0405 0.0945 0.0077 0.078 17.0423 51.3297 3.1843 36 0.5156 0.3875 -0.1848 0.5446 -0.0932 0.3882 -0.0618 0.0785 -0.0253 -0.1014 0.0245 -0.0029 0.0894 0.0089 0.0373 0.0903 -0.0168 -0.0076 0.0953 -0.0017 0.0395 15.0109 32.4495 -14.0777 37 3.1911 0.464 -2.5365 2.0676 -0.434 6.0955 -0.26 0.068 -0.2807 -0.1498 0.0168 0.0777 0.472 -0.2236 0.2433 0.0979 -0.0306 0.0069 0.0472 -0.0176 0.0782 6.6841 15.1707 -3.9477 38 4.1193 1.2703 0.8485 1.8238 0.0633 1.4539 0.0064 0.0584 -0.1576 -0.1214 -0.0442 -0.1895 0.2216 0.1753 0.0378 0.1062 0.02 0.0207 0.0511 0.0112 0.0655 20.1624 18.0746 -3.3681 39 0.5954 -0.5322 0.2301 1.6757 -0.6071 0.6705 -0.0098 0.0486 0.0154 -0.0386 -0.0208 0.0746 -0.0144 -0.0947 0.0306 0.0583 0.0065 -0.0198 0.0957 -0.0004 0.0518 8.5713 42.0883 -7.7439 40 1.9046 -3.9082 2.6855 10.6623 -2.8036 7.3301 -0.0537 -0.196 -0.0199 -0.0409 0.0986 0.2366 0.2027 -0.533 -0.0449 0.111 0.0157 -0.0272 0.1135 0.002 0.0767 3.7026 46.7106 -1.6311
精密化 TLSグループ 大きな表を表示 (5 x 40) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A8 - 31 2 X-RAY DIFFRACTION 2 A32 - 40 3 X-RAY DIFFRACTION 3 A41 - 57 4 X-RAY DIFFRACTION 4 A58 - 75 5 X-RAY DIFFRACTION 5 A76 - 99 6 X-RAY DIFFRACTION 6 A100 - 143 7 X-RAY DIFFRACTION 7 A144 - 174 8 X-RAY DIFFRACTION 8 A175 - 223 9 X-RAY DIFFRACTION 9 A224 - 233 10 X-RAY DIFFRACTION 10 A234 - 251 11 X-RAY DIFFRACTION 11 A252 - 273 12 X-RAY DIFFRACTION 12 A274 - 299 13 X-RAY DIFFRACTION 13 A300 - 339 14 X-RAY DIFFRACTION 14 A340 - 358 15 X-RAY DIFFRACTION 15 A359 - 370 16 X-RAY DIFFRACTION 16 A371 - 402 17 X-RAY DIFFRACTION 17 A403 - 414 18 X-RAY DIFFRACTION 18 A415 - 482 19 X-RAY DIFFRACTION 19 A483 - 502 20 X-RAY DIFFRACTION 20 A503 - 559 21 X-RAY DIFFRACTION 21 B8 - 36 22 X-RAY DIFFRACTION 22 B37 - 57 23 X-RAY DIFFRACTION 23 B58 - 112 24 X-RAY DIFFRACTION 24 B113 - 155 25 X-RAY DIFFRACTION 25 B156 - 186 26 X-RAY DIFFRACTION 26 B187 - 222 27 X-RAY DIFFRACTION 27 B223 - 238 28 X-RAY DIFFRACTION 28 B239 - 263 29 X-RAY DIFFRACTION 29 B264 - 277 30 X-RAY DIFFRACTION 30 B278 - 299 31 X-RAY DIFFRACTION 31 B300 - 339 32 X-RAY DIFFRACTION 32 B340 - 361 33 X-RAY DIFFRACTION 33 B362 - 374 34 X-RAY DIFFRACTION 34 B375 - 402 35 X-RAY DIFFRACTION 35 B403 - 418 36 X-RAY DIFFRACTION 36 B419 - 463 37 X-RAY DIFFRACTION 37 B464 - 475 38 X-RAY DIFFRACTION 38 B476 - 502 39 X-RAY DIFFRACTION 39 B503 - 549 40 X-RAY DIFFRACTION 40 B550 - 559