ソフトウェア 名称 バージョン 分類 HKL-2000データ収集 CNS精密化 PHENIX(phenix.refine: 1.7.3_928)精密化 HKL-2000データ削減 HKL-2000データスケーリング CNS位相決定
精密化 構造決定の手法 : 分子置換開始モデル : PDB ENTRY 3AAB解像度 : 1.9→28.468 Å / Occupancy max : 1 / Occupancy min : 1 / FOM work R set : 0.8436 / SU ML : 0.25 / σ(F) : 0 / 位相誤差 : 22.34 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Selection details Rfree 0.2498 818 5 % RANDOM Rwork 0.2022 - - - obs 0.2045 16345 98.65 % -
溶媒の処理 減衰半径 : 0.98 Å / VDWプローブ半径 : 1.2 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL / Bsol : 56.444 Å2 / ksol : 0.386 e/Å3 原子変位パラメータ Biso max : 129.74 Å2 / Biso mean : 45.8563 Å2 / Biso min : 15.18 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.6309 Å2 -0 Å2 0 Å2 2- - -6.6834 Å2 0 Å2 3- - - 5.0525 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.9→28.468 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 1752 0 0 88 1840
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.01 1782 X-RAY DIFFRACTION f_angle_d1.324 2407 X-RAY DIFFRACTION f_chiral_restr0.09 266 X-RAY DIFFRACTION f_plane_restr0.005 313 X-RAY DIFFRACTION f_dihedral_angle_d14.968 697
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 6
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.9001-2.0191 0.2816 135 0.2497 2489 2624 97 2.0191-2.1749 0.2355 152 0.2125 2517 2669 98 2.1749-2.3937 0.2356 127 0.1957 2570 2697 99 2.3937-2.7398 0.282 113 0.2092 2600 2713 99 2.7398-3.4509 0.2632 151 0.2066 2616 2767 99 3.4509-28.4707 0.2348 140 0.1906 2735 2875 99
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 16) 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 1.2291 0.7972 -1.1397 0.4914 -0.7317 0.9528 0.9106 0.033 0.9494 -0.9155 0.9772 -0.1428 -1.9043 0.3323 -0.288 0.9842 -0.1996 -0.0595 0.5355 0.1483 0.7418 10.4141 25.693 -4.0308 2 1.2816 -1.8011 0.7918 3.4205 -1.5665 0.4438 0.2323 0.1173 0.16 -0.0999 0.0151 0.3378 -0.0194 -0.0678 -0.1517 0.2459 0.0247 -0.0747 0.2911 0.0597 0.2591 6.4042 14.777 2.5316 3 0.5516 -0.7875 0.6262 5.5409 1.0271 1.36 -0.1404 -0.1746 -0.388 0.6203 0.2542 0.312 0.3355 -0.0064 -0.0784 0.2135 0.0161 0.0196 0.2116 0.0786 0.3015 10.7225 0.8071 11.7111 4 3.9458 -0.1938 -0.0854 3.5413 -0.5236 2.5883 0.0091 -0.2833 0.1426 0.3436 0.3925 0.9421 0.072 -0.3941 -0.3222 0.1813 0.0035 0.0486 0.3239 0.1556 0.4006 -0.7586 7.3463 10.8607 5 3.752 -0.9674 -5.0754 0.3066 1.3412 7.3452 -0.5598 0.4617 0.6185 1.4159 -0.0453 1.1189 0.4727 -0.3937 -0.0174 0.4511 0.134 0.1033 0.4752 0.1229 0.8844 5.4365 33.9621 7.7963 6 1.6201 1.0788 0.7787 3.3895 0.3649 0.7273 -0.1023 -0.1143 0.1088 -0.3365 0.1456 0.4569 0.0747 -0.2289 -0.0556 0.2492 0.0053 -0.0895 0.2557 0.0697 0.2923 3.5599 13.0654 4.8507 7 0.8127 1.1289 1.3507 3.2623 1.0916 2.3606 -0.8187 -0.1491 -0.8534 0.937 -0.254 1.1669 0.4546 -0.284 0.1771 0.5761 -0.0021 -0.0237 0.3888 0.019 1.0454 2.1809 -10.3547 7.8778 8 4.3955 4.6816 0.1874 2.0706 0.827 2.7834 0.2049 -0.3372 -0.9647 1.0089 0.1252 -0.4283 0.3763 -0.1802 -0.2111 0.3845 -0.0047 -0.0238 0.408 0.1323 0.3622 8.4549 4.7299 18.8257 9 2.1894 3.0874 0.7621 2.0699 3.1225 3.1458 -0.2027 -0.3521 -0.7437 0.915 0.2147 -0.1907 0.872 0.0588 0.0768 0.3499 0.02 0.0106 0.3194 0.1737 0.401 7.9381 -3.995 14.0805 10 2.0661 3.3314 4.1185 1.8582 4.1808 2.059 1.2951 0.693 0.9914 0.2783 1.2637 -0.2644 -0.4417 -0.5841 -0.1571 0.6662 -0.1628 -0.1895 0.5993 -0.1144 0.3488 10.7017 9.3985 -9.1511 11 3.9871 -1.5769 -0.2759 3.6415 -0.4649 2.2318 0.0995 0.3491 -0.2086 -0.1825 0.0265 -0.2581 0.4325 -0.012 -0.1114 0.2678 0.0272 0.0302 0.2904 -0.0162 0.2033 15.7385 10.3747 0.4264 12 3.3874 0.3695 -0.5533 5.2102 -1.5237 3.1208 0.1209 -0.0298 0.5113 1.0115 0.1249 0.1318 -0.6994 -0.1794 -0.2479 0.3513 0.0361 0.0343 0.2194 0.0095 0.2463 12.5368 26.6457 12.9166 13 3.3266 0.4962 0.423 4.4625 1.0382 2.4793 0.0894 -0.2502 -0.282 0.3548 0.2113 -1.2976 -0.1106 0.4426 -0.314 0.1732 -0.0076 -0.0769 0.2474 -0.0253 0.4328 23.7342 20.0607 11.2919 14 3.0952 2.9253 0.5653 4.7306 2.4596 1.613 0.0308 -0.0472 -0.7794 0.2101 0.2594 -1.0527 0.3482 0.1103 -0.2453 0.2422 0.0376 0.0383 0.2281 0.0398 0.465 17.4216 0.6764 5.5487 15 2.8194 0.8116 0.0572 5.8225 0.0343 3.1589 -0.2271 -0.1965 0.8953 0.2623 -0.1858 -1.2062 -0.6448 -0.1157 0.3018 0.3654 0.0327 -0.1513 0.2293 -0.0402 0.4006 21.1929 31.0142 7.9425 16 0.9033 1.5812 -0.3156 2.1558 -2.3233 0.5417 0.0049 -0.2847 0.3049 1.3643 -0.0832 0.0379 -0.6134 -0.3355 0.2788 0.5653 0.0421 -0.0541 0.2868 -0.0279 0.228 15.0885 26.8677 17.36
精密化 TLSグループ 大きな表を表示 (6 x 16) 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 (resseq 10:16)A10 - 16 2 X-RAY DIFFRACTION 2 chain A and (resseq 17:26)A17 - 26 3 X-RAY DIFFRACTION 3 chain A and (resseq 27:46)A27 - 46 4 X-RAY DIFFRACTION 4 chain A and (resseq 47:70)A47 - 70 5 X-RAY DIFFRACTION 5 chain A and (resseq 71:75)A71 - 75 6 X-RAY DIFFRACTION 6 chain A and (resseq 76:88)A76 - 88 7 X-RAY DIFFRACTION 7 chain A and (resseq 89:98)A89 - 98 8 X-RAY DIFFRACTION 8 chain A and (resseq 99:106)A99 - 106 9 X-RAY DIFFRACTION 9 chain A and (resseq 107:115)A107 - 115 10 X-RAY DIFFRACTION 10 chain B and (resseq 3:11)B3 - 11 11 X-RAY DIFFRACTION 11 chain B and (resseq 12:26)B12 - 26 12 X-RAY DIFFRACTION 12 chain B and (resseq 27:46)B27 - 46 13 X-RAY DIFFRACTION 13 chain B and (resseq 47:70)B47 - 70 14 X-RAY DIFFRACTION 14 chain B and (resseq 71:81)B71 - 81 15 X-RAY DIFFRACTION 15 chain B and (