ソフトウェア 名称 バージョン 分類 Blu-IceMaxデータ収集 PHENIXモデル構築 REFMAC5.7.0032精密化 HKL-3000データ削減 HKL-3000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 : 1.88→27.43 Å / Cor.coef. Fo :Fc : 0.966 / Cor.coef. Fo :Fc free : 0.953 / SU B : 5.664 / SU ML : 0.086 Isotropic thermal model : Thermal Factors Individually Isotropically Refined交差検証法 : THROUGHOUT / ESU R : 0.13 / ESU R Free : 0.124 / 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 0.20746 3360 5.1 % RANDOM Rwork 0.17084 - - - all 0.17268 63040 - - obs 0.17268 63040 99.35 % -
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 : 34.992 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.22 Å2 0 Å2 -0.11 Å2 2- - -0.8 Å2 0 Å2 3- - - 0.58 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.88→27.43 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 5544 0 0 448 5992
拘束条件 大きな表を表示 (5 x 20) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.011 0.019 5812 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 5436 X-RAY DIFFRACTION r_angle_refined_deg1.495 1.936 7890 X-RAY DIFFRACTION r_angle_other_deg0.708 3 12483 X-RAY DIFFRACTION r_dihedral_angle_1_deg3.53 5 696 X-RAY DIFFRACTION r_dihedral_angle_2_deg33.288 24.419 301 X-RAY DIFFRACTION r_dihedral_angle_3_deg9.133 15 942 X-RAY DIFFRACTION r_dihedral_angle_4_deg19.483 15 32 X-RAY DIFFRACTION r_chiral_restr0.089 0.2 822 X-RAY DIFFRACTION r_gen_planes_refined0.007 0.02 6669 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 1439 X-RAY DIFFRACTION r_mcbond_it1.637 1.938 2754 X-RAY DIFFRACTION r_mcbond_other1.638 1.937 2753 X-RAY DIFFRACTION r_mcangle_it2.361 2.894 3460 X-RAY DIFFRACTION r_mcangle_other2.361 2.895 3461 X-RAY DIFFRACTION r_scbond_it2.666 2.245 3058 X-RAY DIFFRACTION r_scbond_other2.662 2.245 3058 X-RAY DIFFRACTION r_scangle_other3.977 3.236 4430 X-RAY DIFFRACTION r_long_range_B_refined6.215 16.923 6833 X-RAY DIFFRACTION r_long_range_B_other6.125 16.389 6640
LS精密化 シェル 解像度 : 1.88→1.929 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.262 240 - Rwork 0.225 4481 - obs - 4481 96.43 %
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 1.0871 -0.2904 0.1123 1.2285 -0.0532 1.2285 0.0069 0.0935 -0.1451 -0.029 -0.0099 0.0609 0.039 -0.0223 0.0029 0.0296 -0.0287 -0.0066 0.0663 -0.0248 0.065 17.6719 9.5004 21.1047 2 3.125 0.8821 0.1737 3.6669 -1.3824 2.9113 0.0032 0.1682 -0.6023 -0.1161 -0.1328 -0.125 0.4825 0.1251 0.1296 0.1637 0.0302 0.0173 0.0371 -0.0726 0.2335 27.4627 -5.8966 19.0568 3 9.4763 -2.7238 4.3133 3.315 -2.4226 6.9271 -0.0461 -0.14 -0.6014 0.0052 0.1186 0.0734 0.3293 -0.1094 -0.0724 0.172 -0.0292 0.0376 0.0334 -0.0599 0.2117 19.944 -2.3901 22.9448 4 1.6696 0.395 0.1154 1.0887 0.312 1.8167 -0.0067 -0.0026 -0.2732 0.0373 -0.0053 -0.0896 0.1764 0.0405 0.012 0.049 -0.0125 -0.0038 0.0193 -0.0133 0.0987 22.728 5.4772 25.5109 5 1.5178 0.8123 1.0283 1.8698 1.4281 3.3513 -0.0404 0.1135 -0.1685 -0.1124 -0.0219 -0.1502 0.0011 0.1539 0.0624 0.0479 0.0023 -0.0044 0.0843 -0.042 0.0967 30.7173 10.6395 19.0262 6 0.7052 0.3029 -0.307 1.2506 -0.6159 1.4054 0.054 -0.1092 -0.0343 0.2245 -0.1159 -0.0358 -0.1695 0.1159 0.0619 0.0748 -0.0064 -0.0392 0.1309 0.0637 0.0855 55.7615 12.9341 35.7411 7 8.5829 -7.8854 1.9367 14.6357 -3.9854 1.0965 0.3174 0.0997 -0.4604 -0.3284 -0.0836 0.9029 0.086 0.032 -0.2337 0.0869 0.0141 -0.0402 0.1413 0.0533 0.1409 43.6346 5.1241 37.6925 8 4.6287 3.1103 0.6407 5.0601 -0.9045 2.3738 0.0134 -0.1092 -0.2656 0.0719 -0.146 -0.2788 0.141 0.1253 0.1327 0.0377 0.0042 -0.0046 0.1255 0.0787 0.0692 58.2294 6.7558 36.5569 9 2.1105 1.1723 0.6901 3.4765 0.3163 1.9526 0.0348 -0.0304 0.0211 0.1131 -0.1065 0.0712 -0.0325 -0.0136 0.0718 0.0114 0.017 -0.0007 0.1221 0.054 0.0685 53.8266 10.7215 27.6619 10 2.0361 0.7617 1.0038 2.9814 1.7683 4.8759 -0.0009 -0.0445 0.0726 0.1389 0.0216 0.0251 -0.3233 -0.1507 -0.0207 0.0751 0.0177 0.0058 0.0899 0.0443 0.0528 47.5832 18.7948 30.0578 11 2.3106 -1.8036 0.5593 2.1859 -0.5275 2.1069 -0.0587 0.2046 0.1862 0.1281 -0.0174 -0.1125 -0.3225 0.2031 0.0761 0.0794 -0.0495 -0.0196 0.1267 0.0816 0.1239 61.9817 25.9092 19.001 12 1.1188 -0.061 0.1413 2.6354 -1.6332 1.564 0.0504 0.2304 -0.0306 -0.4507 -0.0486 0.0585 0.2731 0.015 -0.0017 0.1311 0.0123 -0.0073 0.1698 0.0656 0.0583 53.9096 17.9472 1.196 13 16.9187 9.1226 -6.9779 16.0538 -7.642 4.2302 0.3202 -0.2305 0.2237 0.3406 0.0811 1.0131 -0.1914 0.0333 -0.4013 0.1147 -0.0046 -0.0024 0.2249 0.113 0.1533 44.7975 28.3485 4.7051 14 1.4771 -0.3621 -0.2434 2.3178 -0.8662 2.2146 -0.0107 0.1451 0.126 -0.0699 -0.0737 -0.0782 -0.166 0.0558 0.0844 0.0352 -0.007 -0.0178 0.1394 0.0805 0.0778 56.8032 23.9989 10.6719 15 2.8915 -0.104 -1.6682 3.3313 1.7578 5.2113 -0.0623 0.1108 -0.0843 -0.1268 -0.0177 0.2212 0.1514 -0.1174 0.08 0.0446 -0.0013 -0.0284 0.1419 0.0594 0.0596 47.2488 16.189 13.7676 16 0.8008 -0.0174 0.0018 1.5806 0.3469 1.1904 0.048 -0.023 0.1255 -0.1072 0.0044 -0.0015 -0.1131 -0.0368 -0.0524 0.0451 0.0226 0.0048 0.0651 -0.0204 0.0639 17.1285 23.99 22.6309 17 0.9372 -0.0178 -0.322 8.2449 -3.8117 3.1693 -0.1412 -0.2598 0.6696 0.11 0.161 -0.8406 -0.7361 0.4309 -0.0198 0.4904 -0.137 0.0404 0.2769 -0.1953 0.6381 26.8858 39.7095 27.7622 18 14.6113 -2.981 -2.7089 4.6165 -1.8947 3.9116 0.3819 0.108 0.1049 0.0774 -0.3295 -0.2136 -0.4541 0.4343 -0.0524 0.2761 -0.0497 0.012 0.076 -0.0642 0.2599 25.3811 39.4966 19.9846 19 1.7716 -0.4532 -0.6139 1.5041 0.1471 2.6148 0.0432 0.0236 0.293 -0.183 -0.0275 -0.171 -0.4424 -0.0141 -0.0157 0.1156 0.0025 0.0203 0.0115 -0.0108 0.0953 21.2217 30.1207 19.1131 20 2.5571 -1.3361 -1.3028 1.7539 1.6575 3.4956 0.0436 -0.2165 0.3187 0.0834 0.0587 -0.1433 -0.1406 0.1602 -0.1023 0.0477 -0.0277 0.0216 0.0857 -0.0541 0.1144 30.0891 23.508 25.419
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 - 40 2 X-RAY DIFFRACTION 2 A41 - 78 3 X-RAY DIFFRACTION 3 A79 - 92 4 X-RAY DIFFRACTION 4 A93 - 144 5 X-RAY DIFFRACTION 5 A145 - 167 6 X-RAY DIFFRACTION 6 B0 - 73 7 X-RAY DIFFRACTION 7 B74 - 83 8 X-RAY DIFFRACTION 8 B84 - 108 9 X-RAY DIFFRACTION 9 B109 - 147 10 X-RAY DIFFRACTION 10 B148 - 167 11 X-RAY DIFFRACTION 11 C0 - 23 12 X-RAY DIFFRACTION 12 C24 - 73 13 X-RAY DIFFRACTION 13 C74 - 83 14 X-RAY DIFFRACTION 14 C84 - 144 15 X-RAY DIFFRACTION 15 C145 - 167 16 X-RAY DIFFRACTION 16 D0 - 39 17 X-RAY DIFFRACTION 17 D40 - 65 18 X-RAY DIFFRACTION 18 D66 - 79 19 X-RAY DIFFRACTION 19 D80 - 144 20 X-RAY DIFFRACTION 20 D145 - 167