ソフトウェア 名称 バージョン 分類 NB PHENIX精密化 Show CNS精密化 Show d*TREK9.6Dデータスケーリング Show PDB_EXTRACT3.005 データ抽出 Show Blu-Iceデータ収集 d*TREKデータ削減 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 1N0X解像度 : 2.5→47.955 Å / Occupancy max : 1 / Occupancy min : 1 / SU ML : 0.43 / 交差検証法 : THROUGHOUT / σ(F) : 0.02 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Selection details Rfree 0.252 5622 4.93 % random Rwork 0.203 - - - obs 0.205 114050 94.96 % -
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 : 56.866 Å2 / ksol : 0.374 e/Å3 原子変位パラメータ Biso max : 181.98 Å2 / Biso mean : 66.853 Å2 / Biso min : 29.53 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.274 Å2 -0 Å2 -0 Å2 2- - 2.274 Å2 -0 Å2 3- - - -4.547 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.5→47.955 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 6706 0 64 76 6846
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.008 6917 X-RAY DIFFRACTION f_angle_d1.202 9397 X-RAY DIFFRACTION f_chiral_restr0.077 1055 X-RAY DIFFRACTION f_plane_restr0.005 1195 X-RAY DIFFRACTION f_dihedral_angle_d19.22 2425
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 30
大きな表を表示 (7 x 30) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.5-2.528 0.425 161 0.395 3310 3471 86 2.528-2.558 0.445 166 0.371 3347 3513 89 2.558-2.589 0.377 177 0.366 3433 3610 89 2.589-2.622 0.385 213 0.34 3371 3584 90 2.622-2.657 0.394 184 0.341 3496 3680 91 2.657-2.693 0.368 208 0.323 3473 3681 92 2.693-2.731 0.346 165 0.319 3409 3574 91 2.731-2.772 0.359 216 0.31 3499 3715 92 2.772-2.816 0.299 171 0.284 3553 3724 92 2.816-2.862 0.333 162 0.285 3541 3703 93 2.862-2.911 0.31 185 0.278 3543 3728 94 2.911-2.964 0.282 183 0.264 3553 3736 93 2.964-3.021 0.319 155 0.263 3669 3824 95 3.021-3.083 0.321 227 0.247 3560 3787 95 3.083-3.15 0.278 174 0.226 3699 3873 96 3.15-3.223 0.279 197 0.221 3638 3835 96 3.223-3.303 0.273 159 0.223 3711 3870 97 3.303-3.393 0.249 217 0.214 3667 3884 97 3.393-3.493 0.218 209 0.194 3663 3872 97 3.493-3.605 0.239 185 0.194 3758 3943 98 3.605-3.734 0.242 200 0.192 3717 3917 98 3.734-3.883 0.226 203 0.18 3744 3947 98 3.883-4.06 0.246 155 0.167 3767 3922 98 4.06-4.274 0.192 224 0.145 3691 3915 98 4.274-4.542 0.183 180 0.132 3766 3946 98 4.542-4.892 0.201 191 0.13 3741 3932 99 4.892-5.384 0.154 196 0.129 3796 3992 99 5.384-6.161 0.209 181 0.154 3769 3950 99 6.161-7.757 0.298 162 0.19 3840 4002 99 7.757-47.963 0.215 216 0.193 3704 3920 98
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 40) 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 0.0968 -0.6426 -0.627 1.0691 -1.3912 2.0243 -0.0916 0.1189 0.0758 0.1252 -0.1907 -0.4374 -0.2216 -0.3216 0.3011 0.4001 0.0214 -0.0146 0.4448 0.1116 0.5896 -71.1537 68.1996 -141.7549 2 1.6381 0.4533 -0.2504 2.1887 -3.0938 9.3712 -0.4638 -0.0646 0.0536 0.3162 -0.5081 -0.867 -1.0114 -0.4454 0.8086 0.3578 0.0288 0.0018 0.4002 0.0269 0.5033 -76.9647 70.8707 -141.7761 3 0.9498 -0.8653 -0.0625 0.451 2.4759 3.8144 0.1821 0.2739 -0.1663 0.1656 -0.1667 0.27 0.0213 -0.3395 -0.029 0.2811 0.0908 0.0168 0.4679 0.0552 0.4063 -83.9497 63.5172 -146.9785 4 0.7562 -1.3201 1.5552 0.4446 1.8825 2.7616 -0.1777 -0.394 0.042 -0.0432 -0.0524 0.0065 -0.3168 -0.3145 0.2302 0.3141 0.1204 -0.0166 0.4239 0.0352 0.4428 -83.2684 68.524 -139.2046 5 0.918 -2.2716 0.8694 0.8494 1.0544 -0.2935 0.3966 0.5101 0.0246 -0.2509 -0.2641 0.2902 0.7164 -0.0181 -0.083 0.3639 0.0674 0.018 0.5733 0.0348 0.478 -78.3651 61.982 -146.7585 6 -0.9768 -0.2649 -3.1046 2.1339 1.6488 1.0335 0.1939 0.2387 -0.2957 -0.3552 -0.2349 -0.2365 -0.0189 -0.313 0.0828 0.4041 0.0442 -0.0269 0.6501 0.0394 0.4127 -81.5404 64.9449 -154.2048 7 -0.7792 -0.0187 0.4793 1.3135 -0.4326 1.5079 -0.0835 0.2305 -0.1881 0.1054 0.1216 -0.2312 -0.1017 0.5623 -0.1075 0.3834 -0.0356 0.0196 0.6174 -0.0725 0.494 -55.9441 55.6813 -130.8766 8 0.9024 -0.8518 0.0935 1.9693 -1.2622 1.8281 0.3896 0.1199 0.3502 -0.0238 -0.0554 -0.3113 -0.4913 0.3541 -0.2266 0.3471 -0.1187 0.0582 0.5513 -0.041 0.4722 -50.7201 56.695 -138.0699 9 0.4109 -2.7685 1.0625 1.5777 -0.5146 2.3921 0.2132 0.4171 0.3084 -0.0182 -0.1575 -0.4222 -0.1756 0.583 -0.0234 0.4008 -0.1254 0.0543 0.5708 -0.0317 0.4627 -49.6908 56.3536 -139.3927 10 6.1234 -2.7906 -1.7227 0.0241 -1.3656 2.0085 0.6427 -0.2949 1.2139 -0.0049 -0.188 -0.2809 -0.5618 0.4169 -0.3657 0.5757 -0.226 -0.003 0.6591 -0.1041 0.7608 -49.1781 63.1476 -132.4428 11 0.4542 -0.1895 1.3733 1.607 0.6156 3.6501 -0.6301 -0.1484 0.1856 0.3174 0.5489 0.3684 0.6115 -0.0654 -0.097 0.3102 0.1248 -0.052 0.6761 -0.089 0.5741 -74.4094 43.9518 -156.909 12 -0.1107 0.7764 1.8938 2.0233 0.9437 1.2859 0.7315 0.0998 -0.4719 -0.5493 -0.4539 0.6977 0.1573 0.0952 -0.2457 0.4981 0.163 -0.1424 0.8647 -0.0791 0.6383 -82.2871 48.8373 -164.531 13 1.8594 -0.0553 1.0127 2.514 0.6098 2.0972 0.1765 0.4245 0.4137 0.1327 -0.3026 -0.179 0.3676 0.0948 0.1458 0.3302 0.1312 -0.0359 0.7046 0.0246 0.3669 -73.7899 56.5307 -157.7605 14 0.3901 -3.0669 -0.3135 2.4215 1.6853 1.9577 0.603 0.7448 0.2064 -0.5193 -0.6226 -0.1656 -0.1077 0.3602 0.0519 0.3828 0.1883 0.0189 0.8679 -0.0332 0.3459 -72.2915 53.0412 -164.3935 15 2.2989 -2.0389 0.8501 0.205 0.7771 2.9674 -0.2051 0.3593 -1.1471 0.1961 -0.1726 0.4628 0.0131 -0.4658 0.3381 0.3662 0.0927 0.0406 0.5796 0.0418 0.5821 -80.0465 51.7126 -154.7787 16 0.8404 -0.0359 0.958 1.2196 2.1303 2.8542 0.2469 0.1244 -0.0879 -0.1547 0.3931 -0.6094 -0.2824 0.8952 -0.62 0.2513 0.0405 -0.0001 0.7113 -0.0792 0.4314 -46.29 44.9781 -143.6191 17 0.0837 -0.5141 0.0891 1.8699 0.6574 2.1176 -0.2506 0.0538 0.2686 0.125 0.1325 0.3935 0.3382 0.3072 0.0385 0.1834 0.0352 0.0408 0.5428 -0.0195 0.3056 -48.8717 42.3615 -138.2598 18 5.5406 -1.6563 0.9998 3.2467 -2.1787 3.4866 -0.6047 -0.6309 0.4109 0.2409 0.2488 -0.4008 0.4073 -0.9412 0.2569 0.4778 -0.0381 0.0459 0.8274 -0.0361 0.5366 -49.7829 36.4119 -130.7724 19 0.3272 0.0813 -0.924 0.6928 0.0626 2.2061 0.0697 -0.2449 0.0225 0.0203 0.086 0.2327 -0.3756 -0.9219 -0.2934 0.2651 0.1485 0.0395 0.7141 0.0273 0.4263 -52.2034 46.2711 -142.3095 20 -0.2374 0.9234 2.1364 1.9198 0.2874 3.0803 0.3681 -0.0013 -0.2404 0.3131 0.4852 -0.6712 0.4377 0.4231 -0.5016 0.464 0.0848 -0.0975 0.8902 -0.0784 0.5407 -41.6038 37.0762 -135.386 21 2.8918 1.1777 0.9277 0.1632 0.4055 2.6268 -0.4276 0.0273 -0.3299 -0.038 0.0491 0.0712 0.003 0.5209 0.2997 0.4223 -0.0268 -0.0397 0.4616 -0.0093 0.4952 -33.8806 34.5273 -173.0496 22 2.1506 1.1092 2.3453 0.8905 0.1387 1.897 -0.2333 0.6074 -0.2963 -0.0965 0.1307 0.1428 -0.0112 0.162 0.0464 0.3784 -0.0946 0.0197 0.4275 -0.0483 0.4407 -32.4188 38.2986 -184.1863 23 2.3903 2.8619 1.6788 1.767 -0.7822 4.7331 -0.1731 0.0167 0.2979 0.0652 -0.0183 -0.0729 -0.411 0.2174 0.1633 0.3474 -0.0358 -0.0411 0.3797 0.0073 0.4071 -31.0714 44.8907 -176.9535 24 0.748 1.551 2.9755 4.7938 1.303 1.6321 -0.1895 -0.4483 0.5909 -0.368 0.2028 0.7869 -0.2493 -0.5885 0.0601 0.3042 -0.042 -0.0766 0.3861 -0.0789 0.3466 -40.6221 40.8001 -173.8582 25 2.7142 1.3957 0.3686 1.0883 0.0592 -0.2186 0.2589 0.4428 -0.206 0.5642 -0.2993 -0.555 -0.275 0.4676 0.037 0.5468 -0.1456 -0.0652 0.7118 0.0634 0.5582 -32.2204 44.4449 -192.0644 26 1.9003 -0.4265 1.5262 0.4306 -1.6429 2.6769 0.2411 -0.605 -0.5597 -0.1653 0.276 0.0075 0.1324 0.0329 -0.3928 0.4046 -0.0546 -0.1428 0.3708 0.124 0.5383 -46.8291 28.5759 -166.2665 27 6.2253 1.9136 3.037 3.9727 -0.0051 0.9948 -0.761 0.8772 0.0862 0.2523 0.8799 -0.3538 -0.1924 0.3379 -0.0444 1.4602 -0.0958 -0.4611 1.4913 0.4447 1.3626 -70.5293 11.4959 -171.1925 28 2.5231 -4.1119 -0.0873 -0.2007 -0.7132 2.7894 1.2604 -0.5838 -0.7654 0.1054 -0.0105 -0.3751 0.7838 0.6917 -0.5402 0.4055 0.0523 -0.2575 0.2503 0.2143 0.2567 -54.8487 22.816 -167.3 29 8.2635 -0.7965 2.2115 0.2475 -0.7409 2.6421 0.6624 -0.1894 -1.3965 -0.5772 0.2246 0.4764 0.456 -0.0047 -0.863 0.568 0.0057 -0.2736 0.3446 0.0699 0.6767 -55.7162 21.3301 -171.8281 30 3.1092 1.5965 0.2619 0.319 2.8115 0.6437 0.7784 -0.0961 -1.7917 0.2613 0.0357 -0.7829 1.0113 0.1798 -0.7545 0.9883 -0.0225 -0.4079 0.4805 0.1255 1.058 -50.5791 13.6168 -167.9748 31 -0.4242 1.3634 1.4878 0.9814 1.9712 2.6727 -0.0926 -0.3915 -0.1355 -0.6635 0.0641 -0.0138 -0.8492 -0.0587 -0.0223 0.5805 -0.0949 -0.087 0.4069 0.0669 0.688 -50.6676 52.882 -187.2308 32 1.5302 0.6028 -1.5845 1.45 -3.3583 2.6052 0.1857 0.1723 0.6156 0.3895 0.0271 0.8568 -0.5238 -0.4664 -0.1157 0.6132 -0.061 -0.0822 0.5607 0.0603 0.5853 -60.0985 42.9339 -193.9231 33 4.2514 -2.0772 1.5138 0.745 0.0644 1.0507 -0.0254 0.4848 0.3698 -0.1767 -0.1024 -0.1168 -0.1535 0.2707 0.1083 0.4056 -0.1356 -0.034 0.5076 0.0574 0.4106 -43.5218 45.461 -194.208 34 2.8515 0.6254 0.4551 0.2053 -0.4362 0.2144 -0.1959 1.2115 0.0411 -0.4116 0.0047 0.1205 -0.0423 0.0515 0.1108 0.558 -0.1472 -0.1058 0.7857 0.0622 0.531 -49.0475 42.4741 -199.7869 35 4.4552 1.5905 1.9632 2.8755 1.2958 2.4696 0.2743 0.3089 -1.0235 -0.113 0.1679 -0.991 0.455 0.1899 -0.3767 0.4343 -0.0381 -0.0489 0.4252 -0.0027 0.4182 -54.5343 36.822 -192.3799 36 4.0527 2.4473 0.9366 2.5964 -0.3115 2.3447 0.3097 -0.8657 0.8796 0.1796 -0.4548 0.6382 -0.437 -0.0307 0.0976 0.3915 -0.0553 -0.0597 0.4136 -0.002 0.5329 -46.5294 47.7901 -187.6881 37 3.9705 -0.7554 0.6154 0.1247 0.1327 -0.6097 0.4323 -1.3281 -0.9259 0.0377 -0.3312 -0.073 0.1478 -0.1695 -0.1094 0.4883 -0.3083 -0.2083 0.8424 0.3747 0.5942 -66.1306 21.7587 -168.3299 38 3.6182 0.5662 2.9249 2.2013 0.1581 1.842 0.4229 -0.7793 -0.1449 0.1963 -0.39 -0.1764 -0.206 -0.1715 -0.0484 0.4337 -0.1307 -0.0411 0.5018 -0.0059 0.4021 -68.55 28.913 -172.9278 39 -0.2454 -2.6524 -0.4874 2.1414 -0.963 2.3675 0.2865 -1.3251 -0.6268 0.6694 -0.0573 0.2496 -1.0803 -0.1189 -0.1831 0.6237 -0.4469 -0.1112 1.2379 0.3037 0.4905 -70.5787 24.5241 -160.1013 40 2.5905 -1.7367 1.068 0.4269 -1.0227 5.5732 -0.3269 -0.4407 -1.6207 -0.0277 -0.4913 0.0043 -0.9015 -1.2701 0.4402 0.259 -0.2391 -0.0091 0.5568 0.3946 0.7368 -77.7165 21.7707 -169.3687
精密化 TLSグループ 大きな表を表示 (6 x 40) 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 H and resid 1:13H1 - 13 2 X-RAY DIFFRACTION 2 chain H and resid 14:29H14 - 29 3 X-RAY DIFFRACTION 3 chain H and resid 30:62H30 - 62 4 X-RAY DIFFRACTION 4 chain H and resid 63:83H63 - 83 5 X-RAY DIFFRACTION 5 chain H and resid 84:98H84 - 98 6 X-RAY DIFFRACTION 6 chain H and resid 99:107H99 - 107 7 X-RAY DIFFRACTION 7 chain H and resid 108:129H108 - 129 8 X-RAY DIFFRACTION 8 chain H and resid 130:165H130 - 165 9 X-RAY DIFFRACTION 9 chain H and resid 166:212H166 - 212 10 X-RAY DIFFRACTION 10 chain H and resid 213:228H213 - 228 11 X-RAY DIFFRACTION 11 chain L and resid 1:15L1 - 15 12 X-RAY DIFFRACTION 12 chain L and resid 16:29L16 - 29 13 X-RAY DIFFRACTION 13 chain L and resid 30:47L30 - 47 14 X-RAY DIFFRACTION 14 chain L and resid 48:89L48 - 89 15 X-RAY DIFFRACTION 15 chain L and