ソフトウェア 名称 バージョン 分類 PHENIX(PHENIX.REFINE)精密化 MOSFLMデータ削減 SCALAデータスケーリング PHASER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 1O0V解像度 : 1.75→49.57 Å / SU ML : 0.18 / σ(F) : 1.36 / 位相誤差 : 17.25 / 立体化学のターゲット値 : ML詳細 : 22 TLS GROUPS. REFINEMENT SOFTWARE ADDS THE TLS COMPONENT TO THE ANISOU RECORD OF THE PDB FILE. ATOMIC TEMPERATURE FACTORS WERE NOT REFINED ANISOTROPICALLY.Rfactor 反射数 %反射 Rfree 0.196 2818 5 % Rwork 0.169 - - obs 0.171 56158 99.4 %
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 : 57.4 Å2 / ksol : 0.37 e/Å3 原子変位パラメータ Baniso -1 Baniso -2 Baniso -3 1- 4.2408 Å2 0 Å2 0 Å2 2- - -4.3371 Å2 0 Å2 3- - - 0.0963 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.75→49.57 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3372 0 114 556 4042
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.006 3628 X-RAY DIFFRACTION f_angle_d1.077 4953 X-RAY DIFFRACTION f_dihedral_angle_d19.421 1369 X-RAY DIFFRACTION f_chiral_restr0.073 572 X-RAY DIFFRACTION f_plane_restr0.004 623
LS精密化 シェル 大きな表を表示 (7 x 20) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.75-1.7802 0.248 135 0.2236 2643 X-RAY DIFFRACTION 99 1.7802-1.8126 0.2427 132 0.2127 2624 X-RAY DIFFRACTION 99 1.8126-1.8474 0.2271 144 0.2083 2611 X-RAY DIFFRACTION 100 1.8474-1.8851 0.2348 139 0.1965 2655 X-RAY DIFFRACTION 100 1.8851-1.9261 0.2092 147 0.1787 2648 X-RAY DIFFRACTION 100 1.9261-1.9709 0.1705 121 0.1647 2647 X-RAY DIFFRACTION 100 1.9709-2.0202 0.1796 136 0.1574 2656 X-RAY DIFFRACTION 100 2.0202-2.0748 0.188 146 0.1532 2642 X-RAY DIFFRACTION 100 2.0748-2.1359 0.185 153 0.153 2651 X-RAY DIFFRACTION 100 2.1359-2.2048 0.1825 149 0.1583 2646 X-RAY DIFFRACTION 100 2.2048-2.2836 0.1827 137 0.1564 2672 X-RAY DIFFRACTION 100 2.2836-2.3751 0.1929 151 0.1638 2622 X-RAY DIFFRACTION 100 2.3751-2.4832 0.227 157 0.1706 2689 X-RAY DIFFRACTION 100 2.4832-2.6141 0.206 156 0.1684 2649 X-RAY DIFFRACTION 100 2.6141-2.7778 0.2045 128 0.1681 2717 X-RAY DIFFRACTION 100 2.7778-2.9923 0.2066 131 0.1613 2697 X-RAY DIFFRACTION 100 2.9923-3.2934 0.1755 135 0.1565 2712 X-RAY DIFFRACTION 100 3.2934-3.7698 0.1738 130 0.1484 2725 X-RAY DIFFRACTION 100 3.7698-4.7489 0.1482 137 0.1403 2720 X-RAY DIFFRACTION 99 4.7489-49.5872 0.2183 154 0.2014 2714 X-RAY DIFFRACTION 94
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 22) 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 1.0382 -0.2531 0.3785 1.189 -0.3731 0.7053 -0.0039 -0.1193 -0.2047 0.4559 -0.2309 -0.4557 -0.0859 0.0496 -0.0289 0.1788 0.0106 0.0081 0.2202 0.1175 0.2673 -3.4654 -1.8983 4.937 2 1.4351 0.0981 -0.6055 0.8619 -0.2956 0.4031 0.1828 -0.0585 -0.1399 0.2501 -0.1415 -0.4823 0.2996 0.8108 -0.0003 0.3683 0.063 -0.0448 0.4378 0.1501 0.426 8.9129 -4.1081 11.2523 3 -0.0148 -0.0249 -0.0396 0.1118 0.0819 0.0417 -0.1676 0.8033 0.008 -0.2296 0.037 -0.541 -0.2376 0.3556 0.002 0.7306 -0.1103 0.4346 0.8523 0.2127 0.862 9.683 -2.9934 -5.7904 4 3.8397 -0.6625 -0.3808 2.0774 -0.5014 -0.053 0.1522 0.1708 0.464 0.4776 -0.2953 -0.4286 0.0698 0.7237 -0.0014 0.3313 -0.0208 0.0649 0.1875 0.0692 0.3663 3.2477 0.0482 8.5958 5 1.0982 -0.2091 -1.3394 1.0841 0.0629 1.0283 0.3748 -0.2616 -0.7678 0.4434 -0.187 -0.4733 0.9671 0.3689 0.0075 0.4356 0.0837 -0.0334 0.3507 0.0615 0.468 7.4878 -10.5574 8.8267 6 0.5375 0.3601 0.232 1.9182 0.2738 1.646 -0.0888 -0.022 -0.1099 -0.0927 0.0285 -0.0791 0.177 0.0005 0 0.049 0.0165 0.0259 0.0568 0.0002 0.0338 -27.2168 -3.1792 6.9014 7 1.4642 -0.4051 -0.1503 0.7294 -0.1808 2.4956 0.0386 0.0422 0.0024 -0.1377 -0.0781 -0.214 -0.0528 0.0437 -0.0096 -0.0002 0.018 0.0303 0.0572 -0.0056 0.0146 -21.3082 0.3818 7.4494 8 5.1349 -1.1878 -0.0458 1.8794 -4.3327 4.2435 -0.1261 1.072 -1.7631 -0.7334 0.0652 0.4413 1.9762 -0.1437 0.3163 0.5046 0.0139 0.0788 0.1914 -0.1543 0.4089 -20.7916 -18.1635 1.8151 9 0.7769 0.2735 0.2655 0.6098 -0.1569 1.0297 -0.0394 0.0719 0.1387 -0.0761 -0.0685 -0.097 -0.1337 -0.1903 -0.2388 0.0094 0.0246 0.0466 0.0412 0.0246 -0.0083 -27.6043 5.8736 8.1885 10 0.5609 0.7589 0.6109 1.1552 0.1944 1.8469 -0.0761 0.5245 -0.4242 -0.3524 -0.153 0.2136 -0.0064 -0.3865 -0.0068 0.1252 0.04 0.0134 0.1751 -0.015 0.0656 -26.0837 2.3834 -2.3793 11 0.1358 -1.0486 0.4347 1.5474 -0.3219 1.6555 -0.1 0.2606 0.1485 -0.2306 -0.0656 -0.4872 -0.0168 0.3719 0 0.1006 -0.049 0.0094 0.1788 0.0458 0.1669 -18.4362 -18.4064 32.8963 12 0.6437 0.2686 1.0473 2.4028 -0.5793 1.9936 -0.2337 0.0928 -0.0539 0.3182 -0.0229 -0.8205 0.5139 0.3257 0.0003 0.1667 0.0254 -0.0285 0.2629 0.0376 0.2933 -7.9651 -22.5529 39.9667 13 0.3998 -0.2411 0.5372 0.3585 0.0417 0.2876 0.4685 0.7375 -0.2217 0.0061 -0.4005 -0.3143 0.4861 -0.3833 -0.0005 0.3422 0.0697 0.017 0.1919 -0.0211 0.2644 -10.9852 -29.9234 35.7628 14 1.9424 1.0674 2.2706 3.306 -1.0239 2.1186 -0.1787 0.2792 -0.1885 -0.3022 -0.0392 -0.663 0.2846 0.4938 -0.0444 0.1247 -0.0183 0.0551 0.1619 0.0334 0.1377 -12.9981 -21.7236 34.5366 15 2.3647 -2.2312 0.8848 3.9635 -0.8961 1.0282 0.0025 0.1009 1.0013 -0.0422 -0.1384 -1.6156 -0.1811 0.7995 -0.0137 0.0847 -0.0408 -0.0704 0.3636 -0.0141 0.5944 -3.0467 -17.8543 41.2535 16 1.3463 -0.5375 0.2405 1.8523 -0.2551 0.4395 -0.1372 0.0664 0.0487 -0.1702 -0.009 0.0457 -0.2949 -0.089 -0.004 0.0204 -0.0432 0.004 0.0757 0.0091 0.003 -30.5036 -6.4936 19.0667 17 1.9018 -0.3318 0.2094 1.7836 -0.5077 3.2782 0.007 -0.1242 -0.1383 0.0614 -0.0318 -0.101 0.1322 -0.0461 0.0006 -0.0087 0.0026 -0.0033 0.06 0.0295 -0.0157 -27.7009 -9.5402 19.7887 18 2.1792 -0.0067 -0.0551 -0.2179 -0.0784 0.5049 0.2527 0.0181 -1.0282 -0.6296 0.1166 0.095 0.6666 0.0669 -0.0154 0.2281 -0.1006 -0.0971 0.141 -0.029 0.1836 -39.136 -18.9015 5.5313 19 0.4534 -0.3019 -0.6166 0.9281 -0.0328 0.3517 -0.0203 -0.1502 -0.0876 0.0584 -0.0593 0.1362 0.0713 -0.149 0.0005 0.0156 -0.0468 -0.0174 0.1007 0.0208 0.0579 -37.3887 -12.5786 19.571 20 0.2893 -0.0208 -0.1275 0.8577 0.2252 0.1832 -0.1772 -0.4375 0.0817 0.0773 0.0897 0.3541 -0.7069 -1.1453 -0.001 0.1234 0.0294 -0.01 0.2924 -0.0017 0.1318 -40.7759 -10.2951 21.8895 21 0.0936 0.0055 -0.0506 0.311 0.1392 0.1036 -0.0984 0.0428 -0.0896 -0.3007 0.5406 -1.1111 -0.0963 0.2371 0.0107 0.7758 -0.054 0.2378 0.8606 0.2612 0.4904 -4.8258 -18.0651 24.5497 22 -0.0393 -0.0082 -0.0218 -0.0091 0.0564 0.1184 0.6146 0.083 0.159 -0.0159 0.1813 0.1891 -0.4815 -0.0225 -0.0055 0.7824 -0.1475 0.2826 1.0479 0.1795 0.5353 -1.9941 -3.6186 20.4753
精密化 TLSグループ 大きな表を表示 (4 x 22) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 CHAIN A AND RESID 349:370)2 X-RAY DIFFRACTION 2 CHAIN A AND RESID 371:390)3 X-RAY DIFFRACTION 3 CHAIN A AND RESID 391:396)4 X-RAY DIFFRACTION 4 CHAIN A AND RESID 397:427)5 X-RAY DIFFRACTION 5 CHAIN A AND RESID 428:449)6 X-RAY DIFFRACTION 6 CHAIN A AND RESID 450:486)7 X-RAY DIFFRACTION 7 CHAIN A AND RESID 487:515)8 X-RAY DIFFRACTION 8 CHAIN A AND RESID 516:525)9 X-RAY DIFFRACTION 9 CHAIN A AND RESID 526:550)10 X-RAY DIFFRACTION 10 CHAIN A AND RESID 551:566)11 X-RAY DIFFRACTION 11 CHAIN B AND RESID 349:370)12 X-RAY DIFFRACTION 12 CHAIN B AND RESID 371:395)13 X-RAY DIFFRACTION 13 CHAIN B AND RESID 396:403)14 X-RAY DIFFRACTION 14 CHAIN B AND RESID 404:427)15 X-RAY DIFFRACTION 15 CHAIN B AND RESID 428:444)16 X-RAY DIFFRACTION 16 CHAIN B AND RESID 445:484)17 X-RAY DIFFRACTION 17 CHAIN B AND RESID 485:531)18 X-RAY DIFFRACTION 18 CHAIN B AND