ソフトウェア 名称 バージョン 分類 PHENIX(phenix.refine: 1.5_2)精密化 HKL-2000データ削減 SCALEPACKデータスケーリング PHENIX位相決定
精密化 構造決定の手法 : 単一同系置換・異常分散 / 解像度 : 2.1→33.46 Å / SU ML : 0.23 / σ(F) : 0.03 / 位相誤差 : 18.9 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.209 1593 1.53 % Rwork 0.179 - - obs 0.18 102396 90.3 %
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL / Bsol : 94.73 Å2 / ksol : 0.37 e/Å3 原子変位パラメータ Baniso -1 Baniso -2 Baniso -3 1- -5.2165 Å2 0 Å2 0 Å2 2- - 0.8785 Å2 0 Å2 3- - - 4.338 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.1→33.46 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 9793 0 320 346 10459
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.008 10358 X-RAY DIFFRACTION f_angle_d0.995 14029 X-RAY DIFFRACTION f_dihedral_angle_d17.185 3754 X-RAY DIFFRACTION f_chiral_restr0.073 1689 X-RAY DIFFRACTION f_plane_restr0.004 1642
LS精密化 シェル 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.1-2.1678 0.2951 125 0.2496 8189 X-RAY DIFFRACTION 81 2.1678-2.2452 0.2536 138 0.2137 8633 X-RAY DIFFRACTION 84 2.2452-2.3351 0.1856 137 0.179 8912 X-RAY DIFFRACTION 87 2.3351-2.4414 0.1952 140 0.1636 9033 X-RAY DIFFRACTION 89 2.4414-2.57 0.1982 141 0.1576 9258 X-RAY DIFFRACTION 91 2.57-2.731 0.1743 145 0.1558 9534 X-RAY DIFFRACTION 93 2.731-2.9417 0.2021 160 0.158 9732 X-RAY DIFFRACTION 95 2.9417-3.2375 0.2058 157 0.1596 10004 X-RAY DIFFRACTION 97 3.2375-3.7055 0.1821 156 0.1672 10122 X-RAY DIFFRACTION 98 3.7055-4.6665 0.2002 149 0.1685 9549 X-RAY DIFFRACTION 92 4.6665-33.4605 0.2362 145 0.2086 9431 X-RAY DIFFRACTION 87
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 50) 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 0.1911 -0.1129 0.0464 0.4062 0.1568 0.1113 0.8075 0.8644 1.2471 -1.0357 -0.144 0.2836 0.7128 -0.7811 -0.0072 0.7158 0.1803 0.2036 1.0513 0.2752 0.8611 74.6185 93.4879 84.5046 2 0.3271 -0.2387 0.5861 0.9027 0.2428 1.4798 0.1178 0.0992 0.4912 -0.2795 -0.2021 0.0311 -0.1652 0.2987 0.0002 0.3519 0.0145 0.0418 0.558 0.1171 0.4278 56.6887 77.5034 98.1561 3 2.1087 -1.365 1.2015 1.631 0.8267 3.5289 -0.0071 1.0222 0.5235 -0.0865 0.1384 0.0651 -0.2191 -0.5648 -0.0009 0.2499 0.001 -0.0201 0.3321 0.0424 0.3438 56.7015 75.1512 106.971 4 4.1166 1.878 1.5857 1.5933 0.8253 0.6724 0.9809 0.2415 -1.3132 1.1525 0.493 -0.3878 -0.7314 1.5263 0.0666 1.0496 -0.5552 0.0767 1.1682 0.1334 0.5655 71.149 93.7562 105.0547 5 0.0046 0.0287 0.0081 0.1754 0.0561 0.0137 -0.2158 -0.4057 0.0476 -0.1004 0.0086 1.2153 -1.1854 0.9773 -0.011 1.0302 -0.3518 0.1123 1.0999 -0.4208 1.8962 75.9066 101.4032 102.2917 6 0.3739 0.4639 0.7541 0.7577 1.5854 3.9824 0.2513 -0.6933 -2.2643 -0.4062 1.4958 0.3065 -0.061 2.7276 0.182 0.7743 -0.4405 0.1073 0.9128 0.2424 1.1252 68.5656 98.6028 96.6217 7 1.9184 0.1046 0.4957 1.1792 0.7764 2.7402 0.0562 0.3781 0.297 -0.1096 -0.1274 0.0309 -0.4273 -0.3593 -0.0001 0.3669 0.0355 -0.0015 0.4391 0.1602 0.4307 50.3805 82.8851 101.357 8 0.2131 -0.1189 0.0681 1.0602 0.4769 0.8039 -0.0897 -0.3273 1.0558 -0.4835 1.1605 -1.6824 -1.0099 1.5705 0.0226 0.4385 -0.162 0.0576 0.539 0.0652 0.6487 75.6643 78.9225 110.0954 9 2.3807 -0.7276 -0.0526 1.2294 -0.422 1.6777 0.117 0.4675 0.4155 -0.0185 -0.0388 -0.0179 -0.3178 -0.2806 -0 0.3289 0.0202 0.0257 0.4686 0.147 0.3831 48.6002 82.638 102.1431 10 7.1511 -1.79 7.5512 4.5806 -3.5865 9.5287 0.6824 1.2267 -1.0798 -1.209 -1.0737 -2.3221 -0.2232 3.1844 0.1075 0.5419 -0.4271 -0.1934 0.896 0.2098 1.2488 73.9956 94.4546 115.7166 11 0.0224 0.0356 -0.0172 0.0681 0.0189 0.1013 0.1471 0.2949 -0.1097 -0.9629 -0.1638 0.5719 -1.9101 -1.0613 0 0.8398 -0.253 -0.1898 0.8904 0.2937 1.1713 81.4809 98.047 128.8011 12 0.6067 -0.9657 0.4558 1.5183 -0.6771 2.4402 -0.1188 -0.0258 0.5084 0.0165 -0.1085 -0.2233 -0.4193 0.2554 -0 0.3718 -0.0536 -0.0168 0.2881 0.0061 0.4164 61.259 82.2736 124.1754 13 1.213 -0.9286 -1.0614 3.1396 -1.224 2.5467 -0.0654 0.1201 0.4186 0.1219 0.1268 0.148 -0.2425 -0.015 0.0001 0.3282 -0.0028 -0.0399 0.3267 0.0077 0.2953 59.911 72.5222 124.175 14 7.5785 -2.7583 9.0468 2.803 -3.5527 2.0031 0.4091 -1.6952 -0.2738 0.151 1.1258 -0.2862 -1.1979 -0.6501 0.2036 0.8796 -0.2474 -0.1286 0.5102 -0.3852 1.1493 74.9295 81.8056 134.9352 15 0.0585 0.0322 0.0487 0.0138 0.0364 0.1131 1.3652 -0.7857 -0.0076 -0.1358 -2.4129 -2.1779 -0.2745 0.9289 0.0083 1.8624 0.4121 -0.4136 1.29 0.3237 1.5691 86.2903 86.9149 137.5165 16 2.0018 3.1707 1.9987 2.6815 -1.8791 2.0029 -1.1512 -1.2842 -0.654 0.4188 -2.2002 0.1667 -1.0944 -0.616 -0.4622 1.5533 -0.1099 -0.8502 1.0253 -0.2108 1.0047 76.7768 89.3047 138.5909 17 1.5505 -1.1517 -0.0323 0.8394 -0.2342 2.1078 -0.1189 -0.1902 0.3151 0.3025 0.1177 -0.0489 -0.4292 -0.08 -0 0.4578 -0.0146 -0.0858 0.2454 -0.0766 0.4196 56.7625 81.5338 131.6996 18 0.1231 0.0304 0.0735 0.9515 -0.6812 0.6879 -0.4007 -0.9826 -0.2725 0.2443 -0.05 -1.2167 -0.7183 1.8927 -0.0217 0.2403 -0.0962 -0.0079 0.7104 0.0658 0.6554 80.1572 69.3307 124.4784 19 0.8758 0.201 -0.46 0.8505 0.4733 1.955 -0.0546 0.0178 0.3206 0.2031 -0.0853 -0.0111 -0.2216 -0.0626 -0.0001 0.3942 -0.0277 -0.0632 0.2761 -0.0672 0.3564 55.2706 80.6479 132.3377 20 0.183 -0.0226 -0.1086 0.2516 0.4296 0.7737 -0.1749 -1.0708 -0.1642 -0.1812 -0.4411 -2.081 -2.6338 0.5555 0.0119 0.5637 0.0186 -0.1689 1.185 -0.0762 0.9212 83.9415 69.6124 140.7587 21 0.4231 -0.2105 0.1557 0.1058 -0.0808 0.0632 0.6571 -0.5235 -0.4678 -0.5364 -0.0415 -0.7245 -0.2661 -0.7675 0.0041 1.3521 0.0022 -0.0865 1.4554 0.1318 1.7462 98.3409 58.6978 147.0625 22 0.0316 0.3514 -0.0199 1.9162 0.7231 3.1398 0.0218 -0.3176 -0.2177 0.2303 -0.0657 -0.1724 0.1252 0.2759 -0.0002 0.3424 0.0128 0.0056 0.2842 0.0719 0.3305 66.9201 57.5138 132.3757 23 0.2493 -0.0856 0.1619 0.1142 0.0042 0.1411 -0.071 -0.0998 -1.1844 0.1451 0.922 1.8506 -0.0115 1.0194 0.0004 0.7898 -0.1588 0.1528 1.036 -0.2643 0.688 79.3807 48.0674 134.5174 24 0.0509 -0.0021 0.0728 -0.0003 -0.0009 0.1619 0.3056 0.4704 0.4684 0.0926 0.2283 0.1917 -0.0167 -0.7331 0.0308 0.8215 -0.0018 -0.411 0.9826 -0.2425 1.3836 90.7968 44.9343 132.8974 25 0.0323 -0.05 0.0494 0.0999 -0.1121 0.1282 -0.506 -0.2483 0.5904 -0.2024 0.4975 -0.0848 -1.2579 1.3985 -0.02 2.1011 0.5714 -1.1676 0.9497 -0.4214 3.217 91.3567 42.7248 140.8885 26 0.1035 0.0123 0.0672 0.67 -0.033 0.043 0.4161 1.4786 -2.0623 -1.4812 2.4788 -1.9666 0.3231 0.5502 0.0055 0.7077 0.1605 -0.2323 1.0242 -0.0062 1.6923 85.0741 46.4927 142.313 27 2.1468 -0.1174 -0.8017 1.4514 0.0506 2.7197 -0.1249 -0.2881 -0.2698 0.3714 -0.0479 0.1443 0.2751 0.0047 0.0001 0.4221 0.0555 -0.0011 0.2852 0.0866 0.3108 63.0407 52.0143 138.9881 28 0.1727 -0.0084 0.2048 0.5349 0.0506 0.193 0.1125 0.8657 -0.3969 -0.3823 -0.2346 -0.5701 0.4477 0.4906 -0.0015 0.442 0.0778 0.0223 0.5769 0.0235 0.4912 78.3501 56.1284 118.8325 29 1.0752 0.0413 0.3376 1.1416 -1.8124 2.697 -0.0096 -0.4564 -0.0997 0.2429 0.0518 0.149 0.173 -0.0244 -0 0.416 0.0113 0.0045 0.2827 0.0823 0.3818 60.6665 49.6965 140.6808 30 0.4607 -0.2527 -0.0124 0.2568 0.0938 0.0964 -0.1868 -0.6011 1.0675 1.3662 -0.0755 0.1266 0.2906 2.8872 -0.0156 1.4127 0.4863 0.1682 1.1366 0.0172 1.3741 87.9418 36.5033 121.5791 31 0.1787 0.2668 0.2593 0.3566 0.4004 1.2195 -0.094 -0.422 -0.248 0.1201 0.1586 -0.3212 0.8102 0.6301 -0.0021 0.6915 0.1835 0.0608 0.3995 -0.0427 0.6208 70.0629 37.8353 116.586 32 0.4426 -0.1068 0.547 0.6794 -0.4572 0.8174 0.5152 -0.9205 -0.2535 0.7119 -0.3009 0.4062 0.7544 -0.8663 0.003 0.5438 -0.1589 0.0801 0.5325 -0.0647 0.4872 50.2958 49.6543 112.4953 33 0.1228 0.2324 -0.3295 0.3891 -0.5815 1.1246 -0.1111 0.8649 -1.1893 -0.1312 -0.2779 0.2759 1.0224 0.0594 0.0004 0.5387 0.161 0.0793 0.4357 -0.0835 0.4982 72.2847 43.0466 111.6988 34 0.1361 0.1051 0.1115 0.1164 0.0922 0.0904 -0.8797 -0.5544 -0.1514 0.6599 -1.4893 0.772 0.263 -0.5245 -0.0121 2.1859 1.4721 0.3679 2.1524 0.4279 0.928 83.0086 36.5073 102.2363 35 0.2651 0.2258 0.1478 0.4743 0.1028 0.0854 1.0024 0.4607 -3.0111 -1.4271 -0.6997 1.8901 -1.3816 -0.1034 0.0362 2.9565 0.8596 1.2553 2.1504 0.3101 1.963 85.5854 31.065 96.3288 36 2.3206 -0.6989 -0.9968 7.3725 -4.737 6.9075 -0.5279 0.1999 -0.0641 -0.4383 -1.8997 -0.0231 0.2095 2.0611 -0.8368 1.8002 0.9452 0.468 1.0987 -0.5138 1.6301 80.7326 26.8934 102.7074 37 2.6027 0.4153 0.9959 2.616 -0.2642 1.4723 0.0022 0.042 -0.535 -0.0243 0.0015 0.0136 0.9768 0.086 -0.0001 0.7012 0.06 0.0424 0.0966 -0.0947 0.4928 60.2261 34.9549 113.1162 38 0.1694 0.0347 -0.0966 0.0197 0.0011 0.3075 0.2964 -0.0209 0.0556 -1.3643 0.5105 -1.638 -0.6143 1.5354 0 0.6562 0.0782 0.2449 0.8267 -0.1327 0.6791 78.0851 52.3859 102.0094 39 1.9356 -0.2264 0.1685 0.9474 0.3797 1.525 -0.0421 0.1215 -0.6763 -0.0678 -0.0365 -0.0054 0.8916 0.169 -0.0036 0.762 0.0312 0.0731 0.2364 -0.1347 0.5663 59.3056 35.3382 111.652 40 0.8325 -0.2451 0.6364 0.4932 0.6377 2.2107 0.3178 1.0365 -2.1931 -0.4145 1.2274 -0.1094 2.9033 0.2179 0.0577 0.9588 0.1931 0.289 1.1386 -0.2028 0.8315 79.7398 43.4318 86.4393 41 0.2066 0.0582 -0.0002 0.182 -0.1582 0.1462 -0.4995 0.7634 1.2362 0.5912 0.4893 -1.265 0.3027 -0.5 -0.0183 1.2501 0.3638 0.5989 1.3207 0.2633 1.2252 81.3314 49.448 74.2216 42 0.4115 -0.3628 0.0118 1.8806 -1.105 0.7719 1.2439 0.9643 0.0406 -2.8394 -0.2546 -0.9841 0.2553 -0.6477 0.0265 0.8709 0.0779 0.3293 0.8439 -0.2248 0.6341 73.6607 49.5071 79.7639 43 0.0343 -0.2079 0.1286 1.2842 -0.4549 0.4161 0.0619 1.1911 -0.2882 -0.432 -0.1765 -0.11 0.3252 -0.7126 0.0002 0.4639 -0.0199 0.0267 0.5341 -0.1409 0.4643 57.9186 51.4522 95.6695 44 0.6792 -0.4862 0.3419 2.3727 -0.1188 0.285 0.0241 0.7844 -0.2422 -0.0703 -0.0363 0.0098 0.4252 -0.0552 0.0001 0.3098 -0.025 0.0203 0.5516 -0.0496 0.3149 57.1104 58.2481 100.2282 45 0.0287 -0.1419 -0.0771 0.644 0.2217 0.3158 -0.8822 1.2616 -1.7524 0.3154 -0.0704 0.0938 -0.6249 -0.2565 -0.0024 0.7263 -0.2352 0.1393 1.2146 0.0402 0.8933 75.2699 64.167 78.6282 46 0.1128 0.1755 -0.1397 0.366 -0.1489 0.1831 -0.557 2.3971 0.103 -0.2418 0.5842 -0.7959 -1.9984 -0.4648 0.0044 0.8362 -0.1181 0.0441 1.3493 0.0582 0.574 70.252 60.6909 72.7521 47 1.3305 -0.1043 0.1304 1.3959 -0.0352 2.7121 -0.0094 0.5999 -0.1896 -0.2753 0.0214 0.0631 0.3874 -0.1305 -0 0.3953 -0.0409 0.038 0.5417 -0.0781 0.324 55.9216 56.7557 92.0153 48 7.0446 -6.0342 -2.3369 5.4074 3.2049 6.8429 -0.3192 0.8788 -1.3217 1.2839 0.7945 -0.1354 1.7734 -0.257 -0.1397 0.6501 -0.393 -0.2018 0.9002 -0.4838 0.8504 42.0439 38.2647 89.3341 49 1.1501 -1.1004 1.2554 1.4666 -0.677 2.9482 0.2077 0.6916 -0.3312 -0.107 0.0488 0.5332 0.651 -0.667 -0.0002 0.4503 -0.1058 -0.0238 0.7209 -0.17 0.3429 46.8484 54.8979 85.6627 50 1.8915 -1.331 -0.6351 1.3073 0.7336 0.557 -0.0002 1.5998 -2.2997 -2.775 -0.0187 0.0443 -1.098 -0.6134 -0.0156 0.7505 -0.2865 -0.0178 1.4485 0.6676 1.0509 72.2526 80.479 83.2584
精密化 TLSグループ 大きな表を表示 (6 x 50) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 (chain A and resid 22:31)A22 - 31 2 X-RAY DIFFRACTION 2 (chain A and resid 32:58)A32 - 58 3 X-RAY DIFFRACTION 3 (chain A and resid 59:90)A59 - 90 4 X-RAY DIFFRACTION 4 (chain A and resid 91:99)A91 - 99 5 X-RAY DIFFRACTION 5 (chain A and resid 100:106)A100 - 106 6 X-RAY DIFFRACTION 6 (chain A and resid 107:113)A107 - 113 7 X-RAY DIFFRACTION 7 (chain A and resid 114:178)A114 - 178 8 X-RAY DIFFRACTION 8 (chain A and resid 179:185)A179 - 185 9 X-RAY DIFFRACTION 9 (chain A and resid 186:263)A186 - 263 10 X-RAY DIFFRACTION 10 (chain A and resid 264:278)A264 - 278 11 X-RAY DIFFRACTION 11 (chain B and resid 24:31)B24 - 31 12 X-RAY DIFFRACTION 12 (chain B and resid 32:58)B32 - 58 13 X-RAY DIFFRACTION 13 (chain B and resid 59:88)B59 - 88 14 X-RAY DIFFRACTION 14 (chain B and resid 89:94)B89 - 94 15 X-RAY DIFFRACTION 15 (chain B and