ソフトウェア 名称 バージョン 分類 NB HKL-2000データ削減 Show HKL-2000データスケーリング Show PHASER2.6.1位相決定 Show REFMAC5.8.0135精密化 Show PDB_EXTRACT3.25 データ抽出 Show
精密化 構造決定の手法 : 分子置換開始モデル : 1i9r解像度 : 1.77→50.16 Å / Cor.coef. Fo :Fc : 0.965 / Cor.coef. Fo :Fc free : 0.951 / SU B : 4.987 / SU ML : 0.08 / SU R Cruickshank DPI : 0.122 / 交差検証法 : FREE R-VALUE / σ(F) : 0 / ESU R : 0.122 / ESU R Free : 0.115 詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.2042 1853 4.9 % RANDOM Rwork 0.1693 - - - obs 0.171 36102 98.24 % -
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原子変位パラメータ Biso max : 63.19 Å2 / Biso mean : 24.955 Å2 / Biso min : 11.13 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.09 Å2 0 Å2 0.05 Å2 2- - 0.21 Å2 0 Å2 3- - - -0.13 Å2
精密化ステップ サイクル : final / 解像度 : 1.77→50.16 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3205 0 0 271 3476 Biso mean - - - 30.42 - 残基数 - - - - 434
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.015 0.02 3320 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 2959 X-RAY DIFFRACTION r_angle_refined_deg1.758 1.945 4544 X-RAY DIFFRACTION r_angle_other_deg0.953 3.001 6849 X-RAY DIFFRACTION r_dihedral_angle_1_deg8.671 5.022 445 X-RAY DIFFRACTION r_dihedral_angle_2_deg36.406 24.833 120 X-RAY DIFFRACTION r_dihedral_angle_3_deg12.34 15 489 X-RAY DIFFRACTION r_dihedral_angle_4_deg22.575 15 8 X-RAY DIFFRACTION r_chiral_restr0.1 0.2 521 X-RAY DIFFRACTION r_gen_planes_refined0.003 0.021 3818 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 726
LS精密化 シェル 解像度 : 1.77→1.816 Å / Rfactor Rfree error : 0 / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.223 126 - Rwork 0.2 2607 - all - 2733 - obs - - 96.5 %
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 3.1652 1.5501 -1.8832 3.2205 -2.4455 4.9906 0.0268 0.2612 0.1943 -0.0482 0.0777 0.2118 0.0226 -0.262 -0.1045 0.0816 0.0052 -0.0302 0.1298 0.0727 0.118 -0.8796 7.4562 82.9424 2 4.9588 1.7501 -4.3143 1.6207 -3.3714 7.2221 -0.0304 -0.2103 -0.134 0.0479 -0.1301 -0.0923 -0.0103 0.307 0.1605 0.0964 0.0046 -0.0369 0.0761 0.0032 0.0841 21.0443 -7.3763 117.7273 3 2.931 -0.0675 0.1282 2.1403 -0.8248 6.1864 -0.0258 0.3331 0.0364 -0.2057 0.0732 0.0164 0.3191 -0.0452 -0.0474 0.055 -0.0187 -0.0014 0.0882 -0.0135 0.0448 9.3882 2.6321 78.3288 4 2.4404 0.6287 -1.0341 1.1555 -0.3413 3.3799 -0.0551 0.3445 -0.0797 -0.1218 0.0656 0.0863 0.2611 -0.1354 -0.0105 0.0676 -0.0083 -0.0261 0.0898 0.0003 0.0347 5.1278 1.7061 80.5782 5 4.2017 0.5462 2.3565 1.1128 0.8831 2.8227 -0.0316 0.0275 0.0809 0.1091 0.0228 -0.0461 -0.0425 0.1526 0.0088 0.0279 -0.0102 -0.0045 0.0167 0.0029 0.0166 5.6211 3.2827 115.7692 6 2.1239 -0.0971 -2.2552 1.7734 -1.1657 10.0292 0.0238 -0.1163 0.1142 0.1632 -0.0136 0.0599 -0.231 -0.1256 -0.0102 0.078 -0.031 -0.0004 0.0356 -0.0201 0.0479 5.3566 13.5829 124.0033 7 3.544 2.4698 1.9293 4.5404 3.9605 6.9961 -0.0263 0.1686 -0.0469 -0.1117 0.0048 -0.1282 -0.0344 0.0594 0.0215 0.0226 0.003 0.0065 0.0164 0.0141 0.0489 3.3319 1.6865 103.8786 8 2.9853 1.4337 2.8274 1.3594 2.122 4.1664 0.0861 -0.4557 0.1881 0.2482 -0.1227 0.0529 0.1602 -0.2148 0.0365 0.1189 -0.0224 0.0029 0.1127 -0.0365 0.05 5.2558 6.92 124.9904 9 4.5734 0.0453 -0.1031 4.1333 6.0847 8.9678 0.0079 0.1847 -0.1395 0.3298 0.1553 -0.1198 0.4861 0.2426 -0.1632 0.1405 0.0193 -0.0067 0.0629 0.0343 0.0504 27.7373 1.4234 91.0142 10 4.7873 0.5546 -0.1024 3.9453 1.5662 5.5839 -0.1193 0.3707 0.1887 -0.2169 -0.0913 0.2093 -0.3497 -0.0381 0.2107 0.0683 -0.0293 -0.038 0.0732 0.0312 0.0331 20.2801 9.8759 83.3075 11 4.8303 -2.1245 0.5746 6.1847 1.3962 3.0215 -0.1007 0.7252 0.3221 -0.3714 -0.104 -0.3113 -0.4042 0.5199 0.2047 0.1486 -0.0917 0.0279 0.2963 0.0928 0.0873 30.2466 9.9909 77.2085 12 4.3609 0.479 0.5676 3.9428 2.2178 4.8161 -0.1115 0.3045 0.1671 -0.1815 0.066 -0.0484 -0.2996 0.3079 0.0456 0.0512 -0.022 -0.0102 0.0531 0.0256 0.0173 26.6244 9.5096 86.3741 13 1.1361 0.0872 -0.4981 0.6824 -0.2057 1.7729 0.0298 0.0535 -0.004 -0.045 -0.0342 -0.0997 -0.0964 0.1946 0.0044 0.0284 -0.006 -0.0141 0.039 -0.0061 0.0469 22.9278 5.8586 97.433 14 1.3967 1.1219 -0.5022 3.0105 -0.8903 1.1812 0.0576 -0.1473 -0.0819 0.1394 -0.0658 -0.0226 0.0265 0.1577 0.0082 0.0283 0.0059 -0.0197 0.0363 0.0015 0.0331 15.1583 -1.8927 111.7978 15 8.4215 1.82 -5.7133 9.7459 -4.5312 8.2209 -0.1346 -0.1804 -0.5162 -0.4109 -0.0092 -0.3077 0.1541 0.4679 0.1438 0.0427 0.0012 -0.0131 0.1709 0.0072 0.126 28.9829 3.0535 104.4039 16 3.3991 0.0946 0.5326 4.2178 3.6047 4.988 0.0301 0.4969 -0.2455 0.0266 0.1249 -0.1235 0.1438 0.4747 -0.155 0.0357 0.0171 -0.0078 0.1403 -0.0396 0.0907 31.1948 4.4357 85.9062
精密化 TLSグループ 大きな表を表示 (5 x 16) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 L2 - 26 2 X-RAY DIFFRACTION 2 H212 - 219 3 X-RAY DIFFRACTION 3 L27 - 51 4 X-RAY DIFFRACTION 4 L52 - 110 5 X-RAY DIFFRACTION 5 L111 - 151 6 X-RAY DIFFRACTION 6 L152 - 165 7 X-RAY DIFFRACTION 7 L166 - 179 8 X-RAY DIFFRACTION 8 L180 - 215 9 X-RAY DIFFRACTION 9 H3 - 10 10 X-RAY DIFFRACTION 10 H33 - 50 11 X-RAY DIFFRACTION 11 H51 - 76 12 X-RAY DIFFRACTION 12 H77 - 100 13 X-RAY DIFFRACTION 13 H101 - 130 14 X-RAY DIFFRACTION 14 H131 - 203 15 X-RAY DIFFRACTION 15 H204 - 211 16 X-RAY DIFFRACTION 16 H11 - 32