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-2000データ削減 HKL-2000データスケーリング PHENIX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 3EG7解像度 : 2.882→28.91 Å / Cor.coef. Fo :Fc : 0.96 / Cor.coef. Fo :Fc free : 0.908 / SU B : 39.397 / SU ML : 0.339 / Isotropic thermal model : ISOTROPIC / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R Free : 0.448 / 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 0.27698 1532 5 % RANDOM Rwork 0.18514 - - - obs 0.18973 28867 98.99 % - all - 28867 - -
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 : 84.087 Å2 Baniso -1 Baniso -2 Baniso -3 1- -1.17 Å2 0 Å2 -1 Å2 2- - 4.52 Å2 -0 Å2 3- - - -0.81 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.882→28.91 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8655 0 25 30 8710
拘束条件 大きな表を表示 (5 x 33) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.012 0.019 8897 X-RAY DIFFRACTION r_bond_other_d0.001 0.02 8360 X-RAY DIFFRACTION r_angle_refined_deg1.557 1.937 12017 X-RAY DIFFRACTION r_angle_other_deg0.829 3 19088 X-RAY DIFFRACTION r_dihedral_angle_1_deg7.412 5 1021 X-RAY DIFFRACTION r_dihedral_angle_2_deg35.753 23.955 536 X-RAY DIFFRACTION r_dihedral_angle_3_deg19.965 15 1567 X-RAY DIFFRACTION r_dihedral_angle_4_deg21.955 15 71 X-RAY DIFFRACTION r_chiral_restr0.084 0.2 1264 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 10206 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 2337 X-RAY DIFFRACTION r_nbd_refinedX-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refinedX-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refinedX-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refinedX-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refinedX-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_itX-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_itX-RAY DIFFRACTION r_scbond_itX-RAY DIFFRACTION r_scangle_itX-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
LS精密化 シェル 解像度 : 2.882→2.957 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.354 120 - Rwork 0.288 1942 - obs - - 91.32 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 30) 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 9.7168 3.1533 -6.0972 8.0812 -3.591 12.321 -0.0156 0.5407 1.1959 -0.2027 0.3267 0.1493 -0.9669 0.0858 -0.311 0.2955 0.0687 -0.1151 0.2331 0.0329 0.2438 -2.9198 36.7555 -25.9414 2 21.4762 -1.8895 -14.201 2.8417 5.1051 14.961 0.0705 0.4942 0.746 -0.6765 -0.187 0.4015 -0.9582 -0.5477 0.1165 0.4699 -0.0344 -0.2729 0.2936 -0.075 0.5273 -13.7836 26.0878 -25.1081 3 3.2494 -0.2259 -1.183 5.137 5.4305 6.0526 -0.0718 -0.3845 0.3104 0.0733 -0.1678 0.2747 0.1691 0.0076 0.2396 0.2979 0.1047 -0.014 0.3062 0.0375 0.1264 -2.3353 27.647 -25.351 4 3.0739 0.4891 0.1631 2.5474 -0.2991 1.6177 -0.1706 0.5477 0.8028 -0.1885 0.0743 0.155 -0.6311 -0.3188 0.0963 0.5059 0.0661 -0.068 0.2031 0.131 0.2122 -7.6714 26.3307 -40.7267 5 5.3667 0.3895 -13.7357 7.0647 -2.6319 35.5964 0.5191 0.2292 0.3476 -0.6806 0.1189 -0.4743 -1.0791 -0.5225 -0.638 0.4348 -0.1004 0.0538 0.3986 0.2561 0.3704 8.3744 25.0908 -49.9559 6 5.0882 1.3776 1.0459 8.5463 -1.5329 7.4049 0.2286 0.2918 0.2254 -0.1044 -0.0657 0.3045 -0.7504 -0.1281 -0.1629 0.1257 0.0482 0.0825 0.3005 -0.0228 0.3946 -24.2978 36.8803 -10.7405 7 1.7054 3.7547 -5.9136 8.3003 -13.0571 20.5493 0.6554 0.3607 0.4088 1.6013 0.7096 0.8565 -2.4518 -1.1483 -1.365 0.8096 0.1239 0.0286 0.8587 0.0805 0.7647 -33.435 30.2442 1.1751 8 8.6301 2.123 -0.3371 5.2298 -0.2099 5.0253 0.1702 -0.0876 -0.6634 0.2154 -0.4567 -0.6394 -0.0056 0.4531 0.2865 0.0909 -0.021 0.0671 0.2643 -0.0275 0.2776 -22.0665 28.7902 -7.0674 9 1.0274 0.9947 -0.5346 3.7853 -1.2399 2.017 -0.0461 0.2512 0.1462 -0.2954 0.2005 0.0494 -0.3706 -0.315 -0.1545 0.1675 0.0865 0.0122 0.2636 -0.0088 0.2802 -38.0475 25.4344 -14.0435 10 4.0219 9.3494 -1.9206 21.9949 -4.6773 1.0967 0.1014 -0.0791 0.5124 0.5258 -0.1659 0.8241 -0.2726 -0.0415 0.0645 0.699 0.0893 -0.0959 0.7555 -0.0019 0.8146 -39.0384 26.288 -30.3828 11 0.0183 0.2274 -0.2174 4.1435 -3.8332 3.5564 -0.095 0.0048 0.0769 -1.2379 0.6999 0.5737 1.1712 -0.6313 -0.6049 0.9466 -0.2023 -0.0013 0.7963 -0.0678 0.8592 -22.3099 -16.0027 -32.279 12 8.2521 2.4188 -2.3967 8.6733 -4.0951 5.9012 0.2523 0.2661 -0.1283 -0.0374 -0.317 -0.6187 -0.4404 0.1186 0.0647 0.3254 -0.0059 -0.0028 0.2545 -0.0395 0.1181 -5.5124 -0.9738 -22.8906 13 2.9955 -0.4696 0.3787 5.26 -0.7462 1.5598 -0.1542 0.0749 -0.4385 -0.0636 0.1654 0.4494 0.22 -0.0767 -0.0113 0.2776 -0.0264 0.0184 0.2754 -0.0589 0.1867 -16.2586 -1.661 -33.6969 14 10.3697 2.1006 0.6209 5.3389 -0.0687 0.0811 0.3271 0.638 -1.0265 -0.0515 -0.2064 0.2443 0.0706 -0.0422 -0.1207 0.3014 -0.019 -0.0873 0.3536 -0.0165 0.1744 -11.5899 5.9773 -43.5113 15 11.0838 -3.1291 12.7237 27.7132 -17.1656 21.4751 0.9517 0.1764 -0.1872 -0.6117 -0.5656 0.3636 1.2568 0.4372 -0.3861 0.4189 -0.0227 0.0129 0.8331 -0.2272 0.6323 -30.7584 2.0609 -38.1783 16 11.2865 2.1993 -5.3905 4.3716 -0.3952 11.5015 -0.5298 -0.0374 -0.8987 -0.2065 0.1904 0.1205 1.2387 -0.607 0.3394 0.2175 -0.0475 -0.0724 0.2485 -0.0778 0.3111 -24.9374 -8.4724 -2.8921 17 17.6366 -1.4292 -17.7414 0.5227 0.3236 20.932 -0.2308 0.8561 -0.5771 -0.1433 -0.0672 0.1881 0.6178 -0.7802 0.2979 0.4038 0.0295 -0.2351 0.3253 0.036 0.5169 -25.3287 1.589 -13.4521 18 11.1118 1.3707 -2.4489 13.1656 -2.0236 7.5024 0.371 -0.5743 0.1599 -0.1703 -0.4591 0.2009 0.3234 0.7075 0.0881 0.0647 0.074 -0.0351 0.2277 -0.0923 0.0842 -22.0454 -2.8343 -2.9072 19 1.5029 -0.7664 -0.6194 2.4377 -0.9915 4.7979 0.1015 0.2371 -0.4848 -0.2215 0.1869 0.0835 0.6986 -0.3835 -0.2884 0.1478 -0.0686 -0.0872 0.2322 -0.0686 0.4787 -39.5947 2.0403 -5.9538 20 42.6438 -4.6792 -15.3067 5.4136 -3.3378 10.6727 -0.8013 0.938 -2.124 0.1461 0.1124 0.4153 0.3322 -0.644 0.689 0.4116 -0.3876 0.142 0.4017 -0.114 0.586 -49.7412 2.5371 9.1079 21 5.6763 0.3546 -0.9143 7.218 0.3843 17.747 -0.0192 0.4117 -1.1536 -0.1204 0.1935 -0.5281 0.7143 0.1036 -0.1743 0.3632 -0.0485 0.0888 0.1229 -0.0302 0.3769 17.1534 -8.3511 -20.9372 22 10.8439 2.1855 -0.3826 8.9171 1.6103 9.2726 -0.1942 -0.3195 0.2841 -0.4534 -0.059 -0.1047 0.298 -0.4021 0.2532 0.0592 0.0099 0.05 0.1318 0.1079 0.1878 16.2494 -1.1933 -17.3941 23 3.2085 -5.4858 2.4223 17.8774 -2.8606 5.5432 -0.1385 0.2535 -0.3796 -0.4863 0.2153 -0.3211 0.7029 0.3564 -0.0768 0.3671 -0.1219 0.1097 0.2904 0.0471 0.3175 20.454 -1.7921 -30.099 24 8.5133 0.7964 5.1567 6.2486 0.3627 3.4111 0.3123 0.2888 -0.2658 -1.2761 0.0109 -0.5071 0.6006 0.2261 -0.3232 0.8457 0.1169 -0.02 0.2483 0.0138 0.1892 29.7625 4.608 -31.2383 25 29.4411 2.0736 -9.2691 5.7336 0.9393 10.6663 0.3373 4.4544 -0.607 -0.7697 0.8446 -0.1255 0.8681 -0.0269 -1.1818 1.0246 0.1168 -0.145 0.9637 -0.2886 0.3363 20.739 5.5195 -42.2792 26 12.7706 -0.543 -2.9057 3.2043 -1.5735 8.7688 -0.2703 -0.2772 1.4983 -0.1214 0.1698 -0.2109 -0.9724 0.1978 0.1005 0.3274 0.0244 0.0202 0.1283 -0.0117 0.3627 21.2371 36.5008 -15.7054 27 15.0743 -3.6293 7.3012 9.957 10.9616 21.3609 -0.0456 0.4881 1.2587 -0.1663 0.0285 -0.7451 -0.1959 0.4429 0.0171 0.4153 0.0574 0.1678 0.245 0.0288 0.1948 14.8505 25.4941 -24.6201 28 6.3057 -4.6401 -0.0861 4.7155 1.7429 3.2302 -0.0484 -0.2446 0.3975 0.0252 0.4054 -0.5578 -0.2388 0.0348 -0.357 0.2673 0.0901 0.0228 0.2968 -0.0689 0.2388 21.9371 27.2312 -15.6965 29 3.1136 -0.2718 0.2236 3.4196 1.0041 3.6489 -0.281 0.5102 0.821 -0.1427 0.3831 -1.0023 -0.6163 0.5328 -0.1022 0.2952 -0.0237 0.0621 0.3033 0.0508 0.7553 32.9365 30.0546 -24.9156 30 8.9342 -0.2316 6.9999 2.2234 -0.3019 11.44 -0.6415 0.3017 1.0662 -0.0641 0.1841 -0.7355 -0.1853 0.5905 0.4574 0.2143 0.0446 0.0833 0.2125 0.0749 0.5789 31.7675 20.87 -31.134
精密化 TLSグループ 大きな表を表示 (5 x 30) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A2 - 22 2 X-RAY DIFFRACTION 2 A23 - 36 3 X-RAY DIFFRACTION 3 A37 - 81 4 X-RAY DIFFRACTION 4 A82 - 167 5 X-RAY DIFFRACTION 5 A168 - 173 6 X-RAY DIFFRACTION 6 B2 - 21 7 X-RAY DIFFRACTION 7 B22 - 28 8 X-RAY DIFFRACTION 8 B29 - 67 9 X-RAY DIFFRACTION 9 B68 - 167 10 X-RAY DIFFRACTION 10 B168 - 172 11 X-RAY DIFFRACTION 11 C1 - 6 12 X-RAY DIFFRACTION 12 C7 - 59 13 X-RAY DIFFRACTION 13 C60 - 131 14 X-RAY DIFFRACTION 14 C132 - 167 15 X-RAY DIFFRACTION 15 C168 - 171 16 X-RAY DIFFRACTION 16 D4 - 22 17 X-RAY DIFFRACTION 17 D23 - 36 18 X-RAY DIFFRACTION 18 D37 - 67 19 X-RAY DIFFRACTION 19 D68 - 167 20 X-RAY DIFFRACTION 20 D168 - 173 21 X-RAY DIFFRACTION 21 E2 - 25 22 X-RAY DIFFRACTION 22 E26 - 68 23 X-RAY DIFFRACTION 23 E69 - 108 24 X-RAY DIFFRACTION 24 E109 - 160 25 X-RAY DIFFRACTION 25 E161 - 170 26 X-RAY DIFFRACTION 26 F2 - 22 27 X-RAY DIFFRACTION 27 F23 - 36 28 X-RAY DIFFRACTION 28 F37 - 87 29 X-RAY DIFFRACTION 29 F88 - 139 30 X-RAY DIFFRACTION 30 F140 - 171