ソフトウェア 名称 バージョン 分類 REFMAC5.8.0267精密化 MOSFLMデータ削減 SCALAデータスケーリング MOLREP位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 7VCN解像度 : 2→69.879 Å / Cor.coef. Fo :Fc : 0.963 / Cor.coef. Fo :Fc free : 0.95 / SU B : 11.006 / SU ML : 0.135 / 交差検証法 : FREE R-VALUE / ESU R : 0.173 / ESU R Free : 0.156 / 詳細 : Hydrogens have not been usedRfactor 反射数 %反射 Rfree 0.2339 4294 5.139 % Rwork 0.2009 79271 - all 0.203 - - obs - 83565 90.314 %
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 BULK SOLVENT原子変位パラメータ Biso mean : 57.196 Å2 Baniso -1 Baniso -2 Baniso -3 1- 3.402 Å2 -1.455 Å2 0.52 Å2 2- - -0.696 Å2 0.411 Å2 3- - - -2.472 Å2
精密化ステップ サイクル : LAST / 解像度 : 2→69.879 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 7586 0 0 384 7970
拘束条件 大きな表を表示 (5 x 19) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.012 0.012 7711 X-RAY DIFFRACTION r_angle_refined_deg1.925 1.651 10426 X-RAY DIFFRACTION r_dihedral_angle_1_deg7.078 5 965 X-RAY DIFFRACTION r_dihedral_angle_2_deg39.5 24.684 380 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.642 15 1399 X-RAY DIFFRACTION r_dihedral_angle_4_deg19.342 15 30 X-RAY DIFFRACTION r_chiral_restr0.139 0.2 1051 X-RAY DIFFRACTION r_gen_planes_refined0.012 0.02 5734 X-RAY DIFFRACTION r_nbd_refined0.196 0.2 2697 X-RAY DIFFRACTION r_nbtor_refined0.306 0.2 5250 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.129 0.2 456 X-RAY DIFFRACTION r_symmetry_nbd_refined0.19 0.2 36 X-RAY DIFFRACTION r_symmetry_xyhbond_nbd_refined0.144 0.2 9 X-RAY DIFFRACTION r_mcbond_it4.09 3.408 3881 X-RAY DIFFRACTION r_mcangle_it5.766 5.078 4839 X-RAY DIFFRACTION r_scbond_it5.847 3.902 3830 X-RAY DIFFRACTION r_scangle_it8.553 5.584 5587 X-RAY DIFFRACTION r_lrange_it11.076 64.921 31030 X-RAY DIFFRACTION r_ncsr_local_group_10.084 0.05 14655
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Refine-ID タイプ Rms dev position (Å)Weight position 1 1 AX-RAY DIFFRACTION Local ncs0.08395 0.05008 1 2 BX-RAY DIFFRACTION Local ncs0.08395 0.05008
LS精密化 シェル 大きな表を表示 (7 x 20) 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 (%)2-2.052 0.334 355 0.326 5966 X-RAY DIFFRACTION 92.3313 2.052-2.108 0.318 316 0.306 5812 X-RAY DIFFRACTION 91.7228 2.108-2.169 0.304 332 0.279 5616 X-RAY DIFFRACTION 91.7901 2.169-2.236 0.321 284 0.264 5429 X-RAY DIFFRACTION 90.4242 2.236-2.309 0.294 271 0.265 5147 X-RAY DIFFRACTION 88.9655 2.309-2.39 0.324 238 0.26 4760 X-RAY DIFFRACTION 84.8125 2.39-2.48 0.271 263 0.244 4931 X-RAY DIFFRACTION 90.6457 2.48-2.581 0.271 229 0.216 4878 X-RAY DIFFRACTION 92.939 2.581-2.696 0.253 234 0.204 4594 X-RAY DIFFRACTION 92.3312 2.696-2.828 0.255 235 0.201 4354 X-RAY DIFFRACTION 91.2507 2.828-2.98 0.276 200 0.2 4036 X-RAY DIFFRACTION 89.0852 2.98-3.161 0.253 218 0.212 3587 X-RAY DIFFRACTION 83.7 3.161-3.379 0.245 217 0.212 3775 X-RAY DIFFRACTION 94.0179 3.379-3.649 0.246 190 0.217 3461 X-RAY DIFFRACTION 92.571 3.649-3.996 0.229 158 0.193 3146 X-RAY DIFFRACTION 90.2732 3.996-4.467 0.183 158 0.146 2671 X-RAY DIFFRACTION 86.145 4.467-5.155 0.16 146 0.126 2439 X-RAY DIFFRACTION 88.8927 5.155-6.307 0.197 134 0.161 2149 X-RAY DIFFRACTION 93.2979 6.307-8.893 0.173 74 0.182 1569 X-RAY DIFFRACTION 86.4282 8.893-69.879 0.198 42 0.19 951 X-RAY DIFFRACTION 95.0239
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 8) 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 0.6298 0.5924 -0.1996 1.1526 0.5972 1.0991 -0.1817 -0.2756 -0.1837 -0.2455 -0.0851 -0.0119 -0.041 0.3147 0.2668 0.2066 0.0333 0.0928 0.2265 0.06 0.2204 -18.343 -20.856 -45.354 2 0.0898 0.1322 0.1657 0.9127 1.4671 2.4119 0.039 -0.0053 -0.0806 -0.037 -0.0003 -0.0541 -0.1254 -0.0556 -0.0387 0.213 -0.0868 -0.0496 0.3913 0.0231 0.0792 -21.9596 -0.6606 -25.2497 3 0.8096 0.1621 -0.0344 1.012 0.8327 0.8103 0.1197 0.1231 -0.0073 0.0304 0.0032 -0.1413 0.0009 -0.1942 -0.123 0.193 -0.0473 -0.0079 0.3563 0.0412 0.1176 -19.4262 12.9262 9.2529 4 0.0154 -0.1314 -0.1272 1.902 0.7639 1.6999 0.0136 0.0168 0.0056 0.2097 0.06 -0.2443 -0.4229 -0.4318 -0.0736 0.3306 0.029 -0.0059 0.3819 0.01 0.078 -25.0395 31.7609 41.2808 5 0.1558 -0.155 -0.2694 0.7322 0.1955 0.4962 0.0245 0.0034 0.0084 0.0512 0.0337 -0.0157 -0.0072 0.0211 -0.0582 0.2597 -0.0338 -0.0102 0.1843 -0.0552 0.2121 1.96 12.047 -1.113 6 0.1818 0.1003 0.0374 0.9378 1.3907 2.1747 0.0196 0.0272 0.0494 0.0152 -0.0039 -0.0244 0.0893 -0.072 -0.0157 0.3128 -0.0443 0.016 0.1935 -0.0709 0.1406 9.7058 -11.6195 -19.4064 7 0.39 -0.0267 -0.4729 0.8108 0.8404 1.4291 0.0724 -0.0724 0.0075 -0.0332 -0.0495 -0.037 -0.0288 -0.035 -0.0229 0.3111 -0.0254 0.0065 0.1792 -0.0705 0.1626 9.9318 -25.3947 -53.9478 8 0.0908 0.0428 -0.2123 1.818 -0.6017 0.6873 0.0269 0.0074 0.0576 -0.2067 0.0581 -0.0923 0.0889 -0.1118 -0.085 0.3322 -0.0508 0.0014 0.1834 -0.0465 0.1399 2.6362 -45.1108 -85.6454
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 ALLC40 - 69 2 X-RAY DIFFRACTION 1 ALLB358 - 499 3 X-RAY DIFFRACTION 2 ALLB500 - 604 4 X-RAY DIFFRACTION 3 ALLB605 - 710 5 X-RAY DIFFRACTION 4 ALLB711 - 821 6 X-RAY DIFFRACTION 5 ALLD40 - 69 7 X-RAY DIFFRACTION 5 ALLA358 - 499 8 X-RAY DIFFRACTION 6 ALLA500 - 604 9 X-RAY DIFFRACTION 7 ALLA605 - 710 10 X-RAY DIFFRACTION 8 ALLA711 - 823