ソフトウェア 名称 バージョン 分類 REFMAC5.8.0258精密化 PDB_EXTRACT3.27 データ抽出 XDSデータ削減 PHASER位相決定 XSCALE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 : 4WFE解像度 : 2.782→47.66 Å / Cor.coef. Fo :Fc : 0.889 / Cor.coef. Fo :Fc free : 0.853 / SU B : 45.432 / SU ML : 0.404 / SU R Cruickshank DPI : 0.4575 / 交差検証法 : FREE R-VALUE / σ(F) : 0 / ESU R Free : 0.496 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.2579 1619 4.9 % RANDOM Rwork 0.2145 - - - obs 0.21668 31089 63.21 % -
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 max : 235.86 Å2 / Biso mean : 70.366 Å2 / Biso min : 11.84 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.11 Å2 0 Å2 -0.2 Å2 2- - 2.05 Å2 -0 Å2 3- - - -2.1 Å2
精密化ステップ サイクル : final / 解像度 : 2.782→47.66 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 10398 0 10 188 10596 Biso mean - - 66.62 39.85 - 残基数 - - - - 1351
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.009 0.013 10671 X-RAY DIFFRACTION r_bond_other_d0.001 0.017 9735 X-RAY DIFFRACTION r_angle_refined_deg1.528 1.639 14550 X-RAY DIFFRACTION r_angle_other_deg1.249 1.565 22620 X-RAY DIFFRACTION r_dihedral_angle_1_deg7.288 5 1341 X-RAY DIFFRACTION r_dihedral_angle_2_deg31.172 22.422 446 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.983 15 1691 X-RAY DIFFRACTION r_dihedral_angle_4_deg17.53 15 42 X-RAY DIFFRACTION r_chiral_restr0.062 0.2 1422 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.02 11827 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 2235
Refine LS restraints NCS Refine-ID : X-RAY DIFFRACTION / タイプ : interatomic distance / Weight position : 0.05
Ens-ID Dom-ID Auth asym-ID 数 Rms dev position (Å)1 1 A7335 0.16 1 2 B7335 0.16 2 1 D6233 0.12 2 2 F6233 0.12 3 1 E6237 0.11 3 2 G6237 0.11
LS精密化 シェル 解像度 : 2.782→2.881 Å / Rfactor Rfree error : 0 Rfactor 反射数 %反射 Rfree 0.4617 - - Rwork 0.3992 211 - obs - - 4.09 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 18) 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 2.6096 -0.5352 -2.5618 0.345 0.0761 3.9765 0.2633 0.3184 -0.0715 -0.1901 -0.1943 0.1483 -0.2437 0.458 -0.069 0.4571 -0.0647 0.0302 0.5434 0.02 0.5212 45.6118 -5.5103 9.4513 2 0.2353 -0.0736 0.0476 0.1086 0.6205 7.6969 0.0102 0.5724 -0.1695 -0.1367 -0.1602 0.1613 0.8057 0.3941 0.15 1.5783 0.1502 -0.1192 1.4433 -0.2402 0.9139 50.7053 -19.6775 -21.4899 3 6.7232 2.4866 -1.6904 2.1183 1.1217 5.5785 0.0512 0.5383 -0.5418 -0.3427 0.1892 0.0179 0.8399 -0.3121 -0.2404 1.0799 0.1794 -0.1388 0.8812 -0.0126 0.7857 46.0807 -15.4621 -7.1827 4 2.4293 -0.414 -2.21 0.6811 -0.3781 4.0663 0.3612 0.6127 -0.0362 -0.2721 -0.2258 0.1518 -0.4473 0.2734 -0.1354 0.4547 -0.0272 -0.005 0.6116 -0.0184 0.4459 49.097 -9.8317 6.334 5 2.8893 1.4977 2.3951 6.591 -0.9332 3.0055 -0.45 0.4352 -0.0473 0.5277 0.5165 -0.0108 -0.287 0.2291 -0.0665 0.8371 0.0194 0.0273 0.8401 -0.0513 0.5079 92.9207 -4.2233 -5.1264 6 4.6461 0.3261 -0.5053 3.4784 1.6496 6.3448 0.3117 -0.057 0.7989 -0.1381 -0.2045 -0.6416 -0.9975 0.5017 -0.1072 0.8564 -0.0828 0.0105 0.8854 0.1779 0.6288 66.0072 -3.0367 4.9891 7 3.1168 -0.9698 -0.6175 2.8846 0.2485 5.0125 0.0342 0.367 0.203 -0.5502 -0.2017 0.0521 -0.6602 -0.3603 0.1674 0.2687 0.0295 -0.0131 0.0816 0.0352 0.3443 14.7453 16.312 27.1179 8 4.2415 2.803 3.8669 3.6934 3.9111 6.4443 -0.2122 0.5935 0.2934 -0.8595 0.2816 -0.0698 -1.0778 1.0653 -0.0694 0.4543 -0.0762 0.0402 0.3094 0.0879 0.4839 13.258 45.2876 45.7234 9 2.8539 0.9594 3.7381 3.3373 3.8403 7.4356 -0.278 0.4973 0.2147 -0.2818 0.2473 -0.1809 -0.7429 0.9605 0.0307 0.5106 -0.0812 0.0517 0.3524 0.1389 0.4608 13.8281 46.4969 46.0367 10 3.6836 0.4947 -0.245 4.6279 2.8277 5.6428 -0.0849 -0.0532 0.2668 0.268 0.1327 0.2331 -0.1767 0.2047 -0.0478 0.0902 0.0186 0.0284 0.0272 0.0558 0.3629 25.9407 6.8894 45.2217 11 0.9328 -1.0762 -1.0863 4.3427 2.318 2.1505 -0.0069 -0.258 0.0841 0.2753 0.0617 -0.156 0.0128 0.3079 -0.0548 0.1207 0.02 0.0161 0.1446 0.0568 0.3464 21.2731 19.9151 49.6088 12 6.5469 -3.2277 1.7096 4.0295 -1.0844 2.7543 0.2453 -0.1492 0.1695 0.099 -0.0958 -0.0554 0.038 0.3164 -0.1496 0.2535 -0.0589 -0.0079 0.1436 -0.0045 0.3462 7.4424 36.3926 58.122 13 4.3037 -0.1779 0.3733 3.8858 -1.2707 3.9807 0.2169 -0.3684 -0.4602 0.1826 -0.1158 -0.2251 0.0949 0.0144 -0.1011 0.1551 -0.0297 0.0008 0.0388 0.0145 0.4536 30.783 -35.0585 42.7908 14 7.5538 2.6635 3.6901 3.4445 1.0409 3.826 0.4992 0.726 -0.4063 -0.3081 -0.0877 -0.0434 0.504 0.2368 -0.4115 0.4565 0.0865 -0.0872 0.1573 0.0818 0.5422 10.1401 -63.1358 43.8873 15 7.3322 6.0214 1.047 7.5771 2.4649 5.4521 0.6038 0.2272 -0.3781 0.3056 0.1043 0.421 0.785 -0.1322 -0.7081 0.6488 0.0077 -0.2246 0.0876 0.0839 0.9605 13.6522 -71.5127 46.9568 16 5.9576 1.737 0.4964 5.5209 -0.6553 2.2389 0.0684 0.181 0.0118 0.1685 0.0284 0.1998 0.2993 0.0521 -0.0968 0.2219 -0.0001 0.0357 0.0628 0.0575 0.225 13.1428 -25.7137 30.9128 17 2.8988 1.498 -0.5018 3.1806 -0.6021 0.8531 0.0593 -0.1686 -0.3836 -0.1025 -0.0489 -0.019 0.2024 -0.1717 -0.0105 0.1299 -0.0088 0.0133 0.1067 0.0207 0.4406 5.9855 -44.1517 41.1124 18 2.1873 -1.0007 1.1704 4.1523 -4.2599 8.8896 0.0093 -0.3187 -0.1396 0.0239 0.1186 0.1788 0.4754 -0.0518 -0.1279 0.1962 -0.0553 -0.0455 0.2662 -0.004 0.5391 -2.6216 -55.6548 50.2806
精密化 TLSグループ 大きな表を表示 (5 x 18) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A28 - 148 2 X-RAY DIFFRACTION 2 A149 - 219 3 X-RAY DIFFRACTION 3 A220 - 286 4 X-RAY DIFFRACTION 4 B28 - 175 5 X-RAY DIFFRACTION 5 B176 - 197 6 X-RAY DIFFRACTION 6 B198 - 287 7 X-RAY DIFFRACTION 7 D1 - 105 8 X-RAY DIFFRACTION 8 D106 - 157 9 X-RAY DIFFRACTION 9 D158 - 211 10 X-RAY DIFFRACTION 10 E1 - 80 11 X-RAY DIFFRACTION 11 E81 - 137 12 X-RAY DIFFRACTION 12 E138 - 217 13 X-RAY DIFFRACTION 13 F1 - 105 14 X-RAY DIFFRACTION 14 F106 - 188 15 X-RAY DIFFRACTION 15 F189 - 211 16 X-RAY DIFFRACTION 16 G1 - 80 17 X-RAY DIFFRACTION 17 G81 - 172 18 X-RAY DIFFRACTION 18 G173 - 216