ソフトウェア 名称 バージョン 分類 PHENIX(PHENIX.REFINE: 1.6_289)精密化 MOSFLMデータ削減 SCALAデータスケーリング PHENIX位相決定
精密化 構造決定の手法 : 単波長異常分散開始モデル : NONE
解像度 : 3.2→34.9 Å / SU ML : 0.47 / σ(F) : 1.39 / 位相誤差 : 24.72 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.256 2879 10 % Rwork 0.188 - - obs 0.194 28776 99.9 %
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 : 39.73 Å2 / ksol : 0.31 e/Å3 原子変位パラメータ Baniso -1 Baniso -2 Baniso -3 1- -0.0183 Å2 0 Å2 -2.647 Å2 2- - 3.4314 Å2 0 Å2 3- - - -3.4131 Å2
精密化ステップ サイクル : LAST / 解像度 : 3.2→34.9 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3948 2292 12 56 6308
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.01 6594 X-RAY DIFFRACTION f_angle_d2.66 9411 X-RAY DIFFRACTION f_dihedral_angle_d22.322 2892 X-RAY DIFFRACTION f_chiral_restr0.085 1128 X-RAY DIFFRACTION f_plane_restr0.009 801
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID 数 Refine-ID タイプ Rms dev position (Å)1 1 A1316 X-RAY DIFFRACTION POSITIONAL1 2 B1316 X-RAY DIFFRACTION POSITIONAL0.05 1 3 E1316 X-RAY DIFFRACTION POSITIONAL0.05
LS精密化 シェル 大きな表を表示 (7 x 21) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)3.2-3.2525 0.3657 132 0.2836 1188 X-RAY DIFFRACTION 100 3.2525-3.3085 0.2844 140 0.231 1190 X-RAY DIFFRACTION 100 3.3085-3.3686 0.3058 133 0.2204 1255 X-RAY DIFFRACTION 100 3.3686-3.4333 0.2942 127 0.2297 1262 X-RAY DIFFRACTION 100 3.4333-3.5034 0.2836 152 0.2121 1241 X-RAY DIFFRACTION 100 3.5034-3.5795 0.2884 131 0.2174 1226 X-RAY DIFFRACTION 100 3.5795-3.6626 0.3489 145 0.1966 1194 X-RAY DIFFRACTION 100 3.6626-3.7541 0.241 143 0.1845 1262 X-RAY DIFFRACTION 100 3.7541-3.8555 0.2189 128 0.1811 1272 X-RAY DIFFRACTION 100 3.8555-3.9688 0.2217 140 0.1536 1194 X-RAY DIFFRACTION 100 3.9688-4.0967 0.1962 127 0.1399 1258 X-RAY DIFFRACTION 100 4.0967-4.2429 0.1793 141 0.1363 1249 X-RAY DIFFRACTION 100 4.2429-4.4125 0.2041 143 0.1479 1203 X-RAY DIFFRACTION 100 4.4125-4.6129 0.1876 140 0.1341 1254 X-RAY DIFFRACTION 100 4.6129-4.8555 0.2328 134 0.1479 1220 X-RAY DIFFRACTION 100 4.8555-5.1588 0.2259 133 0.1522 1278 X-RAY DIFFRACTION 100 5.1588-5.5556 0.2297 142 0.1623 1192 X-RAY DIFFRACTION 100 5.5556-6.112 0.2639 140 0.177 1262 X-RAY DIFFRACTION 100 6.112-6.9903 0.2548 140 0.1948 1242 X-RAY DIFFRACTION 100 6.9903-8.7837 0.3067 135 0.1945 1215 X-RAY DIFFRACTION 100 8.7837-34.8988 0.2744 133 0.2152 1240 X-RAY DIFFRACTION 99
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 6) 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 4.8937 -1.8017 0.6642 4.5032 -0.1971 3.6332 -0.0662 0.067 -0.1668 0.0449 -0.1313 -0.2311 0.4373 0.0548 0.1626 0.0934 0.0248 0.0405 0.0982 -0.0469 -0.1331 63.6183 38.535 -6.7206 2 3.5884 0.3468 1.0163 3.1433 0.1355 2.6536 -0.0997 -0.1001 0.4515 -0.3609 -0.0732 0.1056 0.0604 0.2552 0.1736 0.0848 0.0902 -0.0954 0.1045 -0.0689 0.1824 19.1744 66.6467 -17.2619 3 2.2988 0.1293 -0.2741 5.0709 0.9251 4.6074 -0.4176 0.2898 -0.1999 0.2919 -0.1948 1.5515 -0.065 -0.4721 0.2705 0.126 -0.0221 0.1919 0.1646 -0.0892 0.5615 17.01 13.5517 -12.0634 4 6.5261 3.4546 2.2369 2.0576 0.5429 -1.3454 0.1925 -0.0291 -0.4091 -0.1428 0.0481 -0.2606 -0.292 0.0577 0.0105 0.371 -0.1305 0.0329 0.4184 -0.1902 0.221 42.5438 20.6154 -15.3368 5 6.6916 -4.6958 0.3082 1.6884 -2.0698 -2.1496 -0.2866 0.1085 0.2939 -0.2761 -0.0705 0.3691 -0.2548 -0.2863 -0.1966 0.3271 0.105 -0 0.3174 -0.0367 0.0566 46.0558 56.7871 -16.9951 6 1.9539 2.4147 1.2074 4.3079 -1.6573 -1.5181 0.0954 0.1851 -0.7836 -0.7553 -0.2964 -0.3391 -0.0326 -0.1575 0.1156 0.5317 0.0694 0.0086 0.0372 -0.0974 0.4247 14.2577 40.4421 -20.9677
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 CHAIN A2 X-RAY DIFFRACTION 2 CHAIN B3 X-RAY DIFFRACTION 3 CHAIN E4 X-RAY DIFFRACTION 4 CHAIN G5 X-RAY DIFFRACTION 5 CHAIN H6 X-RAY DIFFRACTION 6 CHAIN F