ソフトウェア 名称 バージョン 分類 NB REFMAC5.6.0117精密化 Show PDB_EXTRACT3.11 データ抽出 Show SBC-Collectデータ収集 HKL-3000データ削減 HKL-3000データスケーリング HKL-3000位相決定 MLPHARE位相決定 直接法位相決定 SHELXDE位相決定 ARP/wARPモデル構築 RESOLVE位相決定 Cootモデル構築
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 1.62→63.6 Å / Cor.coef. Fo :Fc : 0.974 / Cor.coef. Fo :Fc free : 0.955 / Occupancy max : 1 / Occupancy min : 0.3 / SU B : 3.584 / SU ML : 0.056 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.118 / ESU R Free : 0.091 立体化学のターゲット値 : MAXIMUM LIKELIHOOD WITH PHASES詳細 : HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.194 2412 5.1 % RANDOM Rwork 0.1362 - - - all 0.1391 47507 - - obs 0.1391 47507 96.05 % -
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 : 67.88 Å2 / Biso mean : 20.7163 Å2 / Biso min : 9.55 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.04 Å2 0.2 Å2 -1.17 Å2 2- - -0.68 Å2 -0.49 Å2 3- - - 1.31 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.62→63.6 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3174 0 34 249 3457
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.011 0.02 3368 X-RAY DIFFRACTION r_angle_refined_deg1.293 1.967 4595 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.886 5 437 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.469 25.319 141 X-RAY DIFFRACTION r_dihedral_angle_3_deg12.22 15 551 X-RAY DIFFRACTION r_dihedral_angle_4_deg18.612 15 13 X-RAY DIFFRACTION r_chiral_restr0.092 0.2 520 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.021 2589 X-RAY DIFFRACTION r_rigid_bond_restr2.361 3 3368 X-RAY DIFFRACTION r_sphericity_free29.274 5 87 X-RAY DIFFRACTION r_sphericity_bonded13.473 5 3461
LS精密化 シェル 解像度 : 1.617→1.659 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.273 172 - Rwork 0.204 3089 - all - 3261 - obs - 3261 89.17 %
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 0.3441 -0.2993 0.4899 1.0196 -1.0552 1.3007 0.0123 -0.0025 -0.0163 -0.0068 0.0233 0.0243 0.0182 -0.0352 -0.0356 0.0123 0.0028 0.0003 0.0212 0.006 0.0025 8.715 37.7285 52.0292 2 0.0094 0.0196 -0.0184 0.1096 -0.1656 0.2735 0.0058 0.0022 -0.0009 0.0009 0.0042 0.0043 0.0063 0.001 -0.01 0.012 0.0025 0.0023 0.0235 0.0079 0.0075 19.1477 32.0813 62.998 3 0.605 -0.2048 0.0221 0.1407 -0.0628 0.0443 0.0082 0.0216 -0.0123 -0.0017 -0.0166 -0.0048 -0.0001 0.0117 0.0084 0.0131 0.0025 0.0038 0.0228 0.0089 0.0057 27.0022 29.1019 61.5555 4 0.0058 0.0141 -0.0186 0.0346 -0.0457 0.0615 -0.0003 0.0013 0.0013 0.0008 0.0038 0.0041 0.0009 -0.0011 -0.0035 0.0118 0.004 0.0032 0.0238 0.0089 0.0081 16.328 41.6184 50.7468 5 0.0151 -0.071 0.1038 0.4008 -0.6549 1.2887 0.0031 -0.0027 -0.0045 0.0009 0.0167 0.0144 0.0003 -0.0216 -0.0198 0.0112 0.0035 0.0019 0.0212 0.0069 0.0079 11.1743 44.0262 56.7343 6 1.546 0.478 -0.6286 0.328 -0.2771 0.392 0.0327 -0.0365 0.0097 0.0265 -0.0156 0.0068 -0.0092 0.0159 -0.0171 0.0131 0.0035 0.0025 0.0196 0.0065 0.0043 17.8581 38.9377 72.5881 7 0.0142 -0.0061 0.0418 0.0405 -0.0143 0.124 0.0002 0.0001 0.0007 0.002 -0.0014 -0.0009 -0.002 -0.002 0.0012 0.0112 0.0028 0.0028 0.0216 0.0081 0.008 22.3997 45.9091 58.5769 8 2.1163 -0.097 -3.521 1.0555 0.6165 6.7597 0.0865 -0.005 0.0297 -0.0515 -0.0046 -0.0027 -0.198 -0.0155 -0.0819 0.0094 0.0029 0.0024 0.0163 0.0078 0.0057 19.1981 59.0851 54.1617 9 0.0691 -0.0329 -0.0125 0.0168 0.006 0.203 -0.0031 -0.0052 0.0046 -0.0001 0.0053 -0.0023 0.0066 0.0081 -0.0022 0.0108 -0.0003 0.0026 0.0194 0.0085 0.0074 28.5599 48.8731 58.6595 10 0.2384 -0.0648 -0.0047 0.0192 0.0278 0.5258 0.0059 0.0155 0.0064 -0.0019 -0.0013 -0.0011 -0.0209 0.0161 -0.0046 0.0113 0.0005 0.0021 0.0202 0.0079 0.0061 30.1275 53.7419 57.7771 11 0.0984 0.0247 -0.0344 0.1177 -0.0711 0.653 0.0004 -0.0025 -0.0074 -0.0051 -0.0044 -0.0074 0.0203 0.0275 0.004 0.0077 0.0038 0.0031 0.0229 0.0081 0.006 36.3991 38.9674 57.2437 12 0.3781 -0.4243 -0.6181 0.9794 0.9172 1.1658 0.0287 -0.0087 0.0286 0.0127 0.0137 -0.0509 -0.013 0.0051 -0.0424 0.0101 0.0008 0.0048 0.0251 0.0049 0.0084 39.5219 55.1508 27.6471 13 0.0868 0.0013 -0.1022 0.0388 0.0747 0.2709 -0.0009 0.0008 0.0012 -0.0019 0.0011 0 -0.0013 0.0052 -0.0002 0.0119 0.0043 0.0019 0.0208 0.0087 0.007 41.3795 43.4175 16.9076 14 0.1702 -0.0032 -0.03 0.3974 -0.0884 0.0257 -0.0072 -0.0042 -0.0065 0.0186 0.0037 -0.0093 -0.0012 0.0027 0.0035 0.0129 0.0047 0.0011 0.0255 0.0078 0.0062 42.8406 35.2706 18.6211 15 0.0823 0.0276 -0.0668 0.0929 0.0328 0.0908 0.0155 -0.0048 0.0103 0.005 -0.0042 -0.0006 -0.0124 0.0023 -0.0113 0.0121 0.0048 0.0019 0.025 0.0087 0.0055 33.7664 49.0299 29.4649 16 0.2283 -0.1426 -0.4646 0.1313 0.2626 1.1418 0.0138 -0.0031 0.0158 0.0006 0.0099 -0.0109 -0.0074 0.0051 -0.0237 0.0115 0.0013 0.002 0.0208 0.0083 0.0066 32.1796 54.2848 23.312 17 0.3687 0.314 -0.143 0.8547 -0.4291 0.2257 -0.0023 0.0294 -0.0157 -0.0209 -0.0045 -0.0182 0.0128 -0.0016 0.0069 0.0102 0.0037 0.0041 0.0225 0.007 0.0057 34.367 45.8982 7.6571 18 0.0058 -0.0127 -0.0015 0.031 0.0121 0.0944 0.0013 0.0025 0.0012 0.0008 0.0004 0.001 -0.0009 0.0012 -0.0018 0.0123 0.0023 0.0029 0.0227 0.0088 0.0079 27.6361 43.7009 22.3064 19 0.7969 0.9221 1.4358 1.1029 1.7302 2.7185 0.0965 -0.0984 0.1269 0.1676 -0.1115 0.0471 0.271 -0.1296 0.015 0.0563 0.0357 -0.0532 0.0915 -0.0674 0.3005 15.6859 49.4725 27.0664 20 0.0686 -0.1033 0.0807 0.1613 -0.0828 0.3985 -0.0032 -0.0012 -0.0012 0.0062 0.0024 0.0015 0.008 -0.0105 0.0009 0.0081 0.0005 0.002 0.0205 0.0097 0.0075 23.5019 38.31 22.7746 21 0.0946 0.0024 0.0709 0.1043 -0.0223 0.3013 0.006 -0.0056 -0.0098 0.01 0.0002 0.0035 0.0056 -0.0168 -0.0062 0.0121 0.0019 0.0037 0.0212 0.008 0.0072 18.4229 37.9181 24.0255 22 0.1811 0.0243 -0.172 0.1374 -0.1814 0.5427 -0.004 -0.0012 -0.0163 -0.0067 -0.0014 0.0002 0.021 0.0121 0.0054 0.0103 0.002 0.0028 0.0182 0.0082 0.0077 31.62 28.5688 24.1659
精密化 TLSグループ 大きな表を表示 (5 x 22) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A-1 - 10 2 X-RAY DIFFRACTION 2 A11 - 33 3 X-RAY DIFFRACTION 3 A34 - 46 4 X-RAY DIFFRACTION 4 A47 - 69 5 X-RAY DIFFRACTION 5 A70 - 89 6 X-RAY DIFFRACTION 6 A90 - 100 7 X-RAY DIFFRACTION 7 A101 - 135 8 X-RAY DIFFRACTION 8 A136 - 141 9 X-RAY DIFFRACTION 9 A142 - 161 10 X-RAY DIFFRACTION 10 A162 - 182 11 X-RAY DIFFRACTION 11 A183 - 207 12 X-RAY DIFFRACTION 12 B-1 - 10 13 X-RAY DIFFRACTION 13 B11 - 33 14 X-RAY DIFFRACTION 14 B34 - 46 15 X-RAY DIFFRACTION 15 B47 - 69 16 X-RAY DIFFRACTION 16 B70 - 89 17 X-RAY DIFFRACTION 17 B90 - 100 18 X-RAY DIFFRACTION 18 B101 - 135 19 X-RAY DIFFRACTION 19 B136 - 141 20 X-RAY DIFFRACTION 20 B142 - 161 21 X-RAY DIFFRACTION 21 B162 - 182 22 X-RAY DIFFRACTION 22 B183 - 207