ソフトウェア 名称 バージョン 分類 NB DENZOデータ削減 Show SCALEPACKデータスケーリング Show REFMAC精密化 Show PDB_EXTRACT3.005 データ抽出 Show MAR345dtbデータ収集 HKL-2000データ削減 HKL-2000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 1TR8解像度 : 2.5→19.56 Å / Cor.coef. Fo :Fc : 0.946 / Cor.coef. Fo :Fc free : 0.928 / WRfactor Rfree : 0.232 / WRfactor Rwork : 0.2 / Occupancy max : 1 / Occupancy min : 1 / FOM work R set : 0.814 / SU B : 16.066 / SU ML : 0.172 / SU R Cruickshank DPI : 0.336 / SU Rfree : 0.251 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.315 / ESU R Free : 0.246 / 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 0.253 529 7.6 % RANDOM Rwork 0.215 - - - obs 0.218 6936 98.48 % -
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 : 68.14 Å2 / Biso mean : 26.468 Å2 / Biso min : 15.75 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.66 Å2 0.83 Å2 0 Å2 2- - 1.66 Å2 0 Å2 3- - - -2.49 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.5→19.56 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 884 0 0 19 903
拘束条件 大きな表を表示 (5 x 17) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.009 0.022 894 X-RAY DIFFRACTION r_angle_refined_deg1.374 1.949 1215 X-RAY DIFFRACTION r_dihedral_angle_1_deg7.117 5 116 X-RAY DIFFRACTION r_dihedral_angle_2_deg39.071 25.946 37 X-RAY DIFFRACTION r_dihedral_angle_3_deg20.047 15 145 X-RAY DIFFRACTION r_dihedral_angle_4_deg27.623 15 3 X-RAY DIFFRACTION r_chiral_restr0.09 0.2 152 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.02 658 X-RAY DIFFRACTION r_nbd_refined0.193 0.2 314 X-RAY DIFFRACTION r_nbtor_refined0.31 0.2 580 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.139 0.2 39 X-RAY DIFFRACTION r_symmetry_vdw_refined0.222 0.2 36 X-RAY DIFFRACTION r_symmetry_hbond_refined0.183 0.2 6 X-RAY DIFFRACTION r_mcbond_it0.46 1.5 598 X-RAY DIFFRACTION r_mcangle_it0.831 2 949 X-RAY DIFFRACTION r_scbond_it0.96 3 318 X-RAY DIFFRACTION r_scangle_it1.442 4.5 266
LS精密化 シェル 解像度 : 2.501→2.566 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.471 29 - Rwork 0.415 403 - all - 432 - obs - - 88.52 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 19) 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 7.9502 10.296 3.5708 23.156 -5.7116 14.7934 -0.1355 -1.1203 1.7579 0.0267 -0.1589 2.3831 0.384 -1.0124 0.2944 0.2048 -0.0225 0.0557 0.2315 -0.0863 0.2947 16.3617 -13.4205 9.8835 2 5.242 -0.2272 -0.75 3.039 -1.811 5.94 -0.2224 0.82 0.2042 0.4714 0.2002 0.031 -0.0007 0.664 0.0221 0.0458 0.0234 -0.0066 0.299 0.0238 0.1109 25.3558 -19.5478 -1.1035 3 6.8804 -4.7014 -4.9002 4.8048 1.4023 5.868 -0.2033 1.1482 0.1578 -1.3565 0.1876 0.0148 0.2207 0.3193 0.0157 0.1557 0.002 0.0306 0.4105 -0.0077 0.1886 26.0921 -23.6609 -8.3801 4 18.6783 -7.1926 -14.9242 10.2495 3.8624 12.3995 0.5013 -0.231 0.4136 -0.2496 -0.5524 -0.834 -1.6465 0.2512 0.0511 0.1614 0.0005 -0.0609 0.31 0.0409 0.2156 20.3862 -12.5695 0.4327 5 11.9386 19.1615 -12.4121 36.0607 -10.6856 28.9793 0.1103 -0.5204 -0.1171 4.2309 1.3347 2.9968 -1.3559 0.5722 -1.445 0.4369 -0.0343 0.0351 0.4694 0.0641 0.5045 12.75 -22.6069 10.4484 6 10.5865 10.0424 -7.1608 43.5049 -45.1961 48.2478 0.296 -1.3165 0.5484 0.3927 -0.4563 0.7492 -0.3222 -0.4949 0.1603 0.145 0.0229 0.0838 0.125 -0.0831 0.1396 14.2123 -19.4163 3.4273 7 33.6207 -25.3004 -9.6206 19.7471 11.767 31.7046 -0.1577 3.0069 2.6854 -0.1483 -0.3279 -1.6366 -1.9538 -0.2314 0.4856 0.2612 -0.0684 0.0506 0.3387 0.2026 0.2878 22.9138 -14.7477 -8.6434 8 4.1495 -0.9426 7.5015 2.5464 7.3896 49.0164 0.0771 1.1126 1.3393 -1.1449 -0.1629 -0.3403 -0.5287 0.6237 0.0858 0.0921 0.0298 0.082 0.417 0.0778 0.1826 33.4394 -20.1029 -9.1656 9 14.6413 0.5256 -7.7624 0.0375 -0.3207 4.2102 -0.3865 -0.1833 0.0114 0.1026 -0.1388 -0.8205 -0.3681 0.1343 0.5253 0.0177 -0.015 0.0198 0.25 0.0066 0.2125 35.8259 -20.8634 0.0651 10 10.9707 6.0098 1.611 3.382 -1.3348 54.9808 0.4544 1.2775 -2.1307 -1.4158 -1.7606 -1.4777 1.8767 0.4596 1.3062 0.173 0.2086 0.0305 0.3561 -0.1277 0.6489 33.4454 -30.901 -1.5053 11 17.5919 6.0256 -5.7428 7.8471 7.7807 18.3046 -0.9196 0.0671 0.0412 0.2237 0.4164 0.802 -0.2909 0.0403 0.5032 0.1262 -0.0526 0.0009 0.2307 -0.0223 0.113 9.9775 -26.288 -8.1028 12 12.3588 1.5413 1.4477 7.1583 3.3777 1.6369 -0.4435 0.1762 -0.4618 -0.4263 0.2785 -0.0958 0.3336 0.5686 0.165 0.0749 0.0292 0.0515 0.1998 -0.0071 0.1721 24.1422 -27.0986 -0.8287 13 1.8597 -0.4463 5.3924 2.2227 -2.3269 16.1406 0.2354 0.4721 0.6738 0.4526 -0.1354 0.0631 -0.5848 0.3366 -0.1 0.1822 -0.0164 0.0076 0.2015 -0.016 0.2994 27.4739 -14.8448 8.6888 14 13.4426 0.6227 6.2929 0.6608 -1.2229 6.5747 0.2961 0.032 -0.3952 -0.0049 -0.1734 -0.0798 -0.1479 -0.1896 -0.1227 0.1347 -0.0169 0.0848 0.1946 -0.0019 0.1547 24.8173 -22.0987 8.4215 15 28.7915 4.3164 3.346 3.2507 4.5784 6.7724 0.2521 -0.5563 -1.483 0.2925 0.1578 -0.132 0.8156 -0.7741 -0.4099 0.1276 -0.0753 0.006 0.2894 -0.0359 0.2292 16.7515 -29.2398 -0.4033 16 2.3249 -0.2996 2.6076 0.0386 -0.3361 2.9246 -0.3061 -0.5441 1.5401 -1.6386 -0.7068 1.6811 -1.1325 0.6279 1.013 0.4206 -0.0035 -0.1203 0.6251 0.1179 0.5381 10.1767 -17.6227 -7.5396 17 4.9938 2.7541 -2.662 20.8462 -18.8046 19.3399 0.0273 0.1953 -0.0422 -0.2083 0.376 0.8776 0.1015 0.4402 -0.4033 0.0325 -0.0374 -0.0029 0.2664 -0.0853 0.2612 14.2764 -24.6124 0.9335 18 21.3843 4.1057 3.0724 4.9826 1.8656 8.7612 0.8639 -0.3235 -0.8288 -0.2349 -0.6091 -0.0881 0.6634 -0.3844 -0.2548 0.182 0.016 -0.0077 0.2455 0.0587 0.135 26.1596 -25.4378 11.6907 19 42.4019 -8.6758 4.0555 15.5066 1.6394 2.3594 -0.4483 -1.751 0.2234 1.3368 0.5944 -0.4737 0.0248 1.0611 -0.1461 0.1537 0.0425 0.0315 0.3888 -0.0089 0.1074 38.793 -22.2063 12.2763
精密化 TLSグループ 大きな表を表示 (5 x 19) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A25 - 31 2 X-RAY DIFFRACTION 2 A32 - 38 3 X-RAY DIFFRACTION 3 A39 - 45 4 X-RAY DIFFRACTION 4 A46 - 51 5 X-RAY DIFFRACTION 5 A52 - 58 6 X-RAY DIFFRACTION 6 A59 - 63 7 X-RAY DIFFRACTION 7 A64 - 69 8 X-RAY DIFFRACTION 8 A70 - 74 9 X-RAY DIFFRACTION 9 A75 - 81 10 X-RAY DIFFRACTION 10 A82 - 88 11 X-RAY DIFFRACTION 11 B24 - 30 12 X-RAY DIFFRACTION 12 B31 - 36 13 X-RAY DIFFRACTION 13 B37 - 42 14 X-RAY DIFFRACTION 14 B43 - 47 15 X-RAY DIFFRACTION 15 B48 - 53 16 X-RAY DIFFRACTION 16 B54 - 60 17 X-RAY DIFFRACTION 17 B61 - 65 18 X-RAY DIFFRACTION 18 B66 - 71 19 X-RAY DIFFRACTION 19 B72 - 77