ソフトウェア 名称 バージョン 分類 PHENIX1-9-1692 精密化 XSCALENovember 3, 2014データスケーリング PHASER2.5.6位相決定 PDB_EXTRACT3.15 データ抽出
精密化 構造決定の手法 : 分子置換開始モデル : 4O4O解像度 : 1.8→43.918 Å / SU ML : 0.24 / 交差検証法 : FREE R-VALUE / σ(F) : 1.32 / 位相誤差 : 29.7 Rfactor 反射数 %反射 Selection details Rfree 0.2283 3027 5.02 % Random selection Rwork 0.2071 - - - obs 0.2082 60319 97.87 % -
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å原子変位パラメータ Biso max : 164.9 Å2 / Biso mean : 59.5374 Å2 / Biso min : 31.01 Å2 精密化ステップ サイクル : final / 解像度 : 1.8→43.918 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2306 0 9 77 2392 Biso mean - - 55.63 47.82 - 残基数 - - - - 272
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.007 2398 X-RAY DIFFRACTION f_angle_d1.088 3255 X-RAY DIFFRACTION f_chiral_restr0.046 308 X-RAY DIFFRACTION f_plane_restr0.005 419 X-RAY DIFFRACTION f_dihedral_angle_d14.713 842
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID 数 Refine-ID タイプ Rms dev position (Å)1 1 A1153 X-RAY DIFFRACTION POSITIONAL0.015 1 2 B1153 X-RAY DIFFRACTION POSITIONAL0.015
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 10
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.8-1.8643 0.3784 295 0.3744 5671 5966 96 1.8643-1.9389 0.344 298 0.3238 5608 5906 96 1.9389-2.0272 0.2881 300 0.2619 5676 5976 97 2.0272-2.1341 0.2983 301 0.2542 5707 6008 98 2.1341-2.2678 0.2677 301 0.2273 5751 6052 98 2.2678-2.4429 0.2539 304 0.2315 5761 6065 98 2.4429-2.6887 0.2997 304 0.2295 5714 6018 98 2.6887-3.0776 0.2555 306 0.2337 5771 6077 99 3.0776-3.8771 0.238 310 0.1941 5829 6139 99 3.8771-43.9311 0.1602 308 0.1664 5804 6112 99
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 21) 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 4.1534 -1.3175 0.5149 4.1674 0.4648 1.6807 0.7058 -1.1455 1.1358 1.0953 -0.1725 -1.0307 -0.9364 1.2396 -0.4716 0.5224 -0.1563 -0.0265 0.7638 -0.1514 0.4247 65.2928 23.8618 30.1048 2 6.923 1.1116 -2.2561 3.0697 0.0176 2.702 0.0253 0.3882 0.0985 0.1409 0.1497 -0.2101 0.1542 0.6172 -0.4458 0.4493 0.0207 0.0252 0.4945 0.0205 0.3942 68.9559 19.2891 9.3458 3 9.1993 -3.1612 -4.5732 7.8533 2.8942 7.2983 0.307 0.3436 0.3698 -0.3967 -0.1398 -0.2461 -0.4065 0.0922 -0.0989 0.3608 -0.028 0.0061 0.4028 0.0152 0.3732 62.0896 19.2447 11.7073 4 8.318 -1.6195 -5.5027 3.7467 2.2705 4.0437 0.2046 0.8584 0.077 0.0519 -0.2987 0.018 -0.1917 -1.1748 0.1155 0.3709 0.0123 0.0106 0.4087 -0.0154 0.3618 55.3379 20.8036 13.3425 5 8.6424 -0.6544 3.6407 5.9336 -2.9185 2.8669 0.013 -0.789 0.3025 0.7857 -0.3284 -0.1451 0.8323 0.4881 0.2693 0.6016 0 0.0327 0.6816 -0.0778 0.3358 57.678 17.6077 33.4858 6 4.3325 2.097 5.8469 3.5168 3.278 8.1816 0.0697 -1.3448 -0.359 0.1296 0.1428 -0.1551 -0.2749 -0.1898 -0.1824 0.363 -0.0118 0.0141 0.6237 0.0192 0.3314 54.4292 13.5503 27.7935 7 2.2153 -1.1406 2.2288 8.8657 -0.8483 3.485 -0.3272 0.2022 -0.1211 0.4456 -0.154 -1.2912 -0.0458 1.2295 0.485 0.4174 -0.0521 -0.0934 0.7297 0.1048 0.5085 68.1054 14.1408 29.7439 8 9.4058 6.7037 0.3003 8.3551 3.7757 7.8283 0.3012 0.5323 -1.0911 0.0683 -0.0527 0.5138 0.1026 -0.0845 -0.1164 0.429 0.0625 -0.0379 0.4896 0.1082 0.6069 56.3616 6.5004 23.8408 9 8.7558 5.7815 1.3361 9.6097 3.4311 9.7375 -0.3534 1.2546 -0.5424 0.4762 0.7917 0.0732 0.343 -0.3035 -0.2213 0.5169 0.0474 0.0276 0.589 -0.0237 0.342 58.0972 5.9803 18.9601 10 9.8616 5.6129 5.6672 3.4998 4.2162 8.0273 -0.1734 -0.1514 -0.6096 -0.3597 0.2149 -1.0214 0.3037 0.75 0.0947 0.4428 -0.0216 0.0256 0.535 -0.1046 0.5021 68.0906 14.9777 19.3416 11 2.9026 2.8376 -4.1785 4.9767 -4.7797 6.2267 -0.5876 2.2725 -0.207 -1.2018 0.8941 0.9803 2.0516 -1.24 -0.2659 0.9032 -0.2602 -0.0401 1.0014 -0.0838 0.7886 59.6321 1.8769 12.6477 12 2.4172 1.7295 1.5476 4.2081 5.7022 8.0747 -0.2408 0.061 0.7206 -0.7399 0.7225 -0.181 -0.6438 1.1443 -0.5059 0.4037 -0.0799 0.1004 0.5754 -0.0054 0.4485 68.9651 20.2353 13.7902 13 4.4136 -1.2116 -0.334 4.5243 0.1271 6.389 0.4606 -1.0613 -0.9724 1.1539 0.0872 0.8056 1.0443 -1.4621 -0.4947 0.5283 -0.1659 0.0302 0.7864 0.1608 0.4476 29.6748 8.5365 30.1087 14 7.8504 0.0436 3.3006 3.751 -1.223 7.9475 0.2063 0.1521 -0.2756 -0.2354 0.0127 0.3514 0.2567 -0.4977 -0.1577 0.3673 -0.0113 -0.0053 0.3786 -0.02 0.3522 29.7354 13.1332 10.6333 15 8.4882 -1.0181 5.4739 3.5149 -1.9223 4.0063 0.1809 0.8594 -0.0793 0.0312 -0.2129 0.0063 0.247 1.1618 -0.0293 0.3649 0.0156 -0.0001 0.384 0.017 0.3523 39.6129 11.5948 13.3364 16 3.3301 0.5147 -1.62 4.8003 -0.4992 6.0114 -0.0119 -0.7362 -0.0517 0.5184 0.1598 0.0474 -0.0998 -0.3917 -0.0483 0.4153 -0.0128 -0.0231 0.605 0.0351 0.3167 38.8593 16.7467 30.741 17 2.1688 -1.4644 -1.9378 8.0404 0.5747 2.0577 -0.3915 0.1298 0.0523 0.5706 -0.1024 1.2126 0.0879 -0.9601 0.5812 0.4366 -0.0563 0.1274 0.7579 -0.1065 0.5142 26.8645 18.2563 29.747 18 8.9241 7.6045 -0.8528 9.3788 -3.2227 9.4757 -0.248 0.638 0.8264 -0.1386 0.376 -0.1711 -0.3124 0.1702 -0.0653 0.4417 0.0627 0.0119 0.4967 -0.0189 0.5002 37.7737 26.1449 21.5181 19 5.2464 5.4174 -5.1121 5.708 -5.1328 5.087 -0.2174 0.1381 0.6177 -0.6889 0.364 1.1286 -0.0367 -0.77 -0.0295 0.4414 -0.0356 -0.013 0.5955 0.1139 0.5088 26.8666 17.4235 19.3475 20 4.6598 5.207 2.3632 5.9227 2.6175 2.4849 -1.0429 1.1567 -0.288 -1.807 0.5962 -1.2131 -1.3975 1.7917 0.6027 0.7915 -0.2794 0.0238 1.1023 0.0979 0.837 35.3203 30.5213 12.6424 21 8.5297 1.9672 -1.7235 3.2375 -5.3338 9.2647 -0.1232 -0.0237 -0.5501 -0.9009 0.4343 0.4128 0.6039 -1.0075 -0.2633 0.3704 -0.0778 -0.0982 0.5846 0.0164 0.3817 25.9912 12.163 13.7974
精密化 TLSグループ 大きな表を表示 (6 x 21) 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 'A' and (resid -1 through 9 ) A0 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 10 through 22 )A0 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 23 through 37 )A0 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 38 through 57 )A0 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 58 through 67 )A0 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 68 through 77 )A0 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 78 through 87 )A0 8 X-RAY DIFFRACTION 8 chain 'A' and (resid 88 through 97 )A0 9 X-RAY DIFFRACTION 9 chain 'A' and (resid 98 through 107 )A0 10 X-RAY DIFFRACTION 10 chain 'A' and (resid 108 through 117 )A0 11 X-RAY DIFFRACTION 11 chain 'A' and (resid 118 through 127 )A0 12 X-RAY DIFFRACTION 12 chain 'A' and (resid 128 through 134 )A0 13 X-RAY DIFFRACTION 13 chain 'B' and (resid -1 through 9 ) B0 14 X-RAY DIFFRACTION 14 chain 'B' and (resid 10 through 37 )B0 15 X-RAY DIFFRACTION 15 chain 'B' and (resid