ソフトウェア 名称 バージョン 分類 PHENIX1.20_4444精密化 autoPROC1.19.2_4158data processing XDSデータ削減 Aimlessデータスケーリング PHASER位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 2VLH解像度 : 1.37→45.27 Å / SU ML : 0.1659 / 交差検証法 : FREE R-VALUE / σ(F) : 1.96 / 位相誤差 : 19.1939 立体化学のターゲット値 : GeoStd + Monomer Library + CDL v1.2Rfactor 反射数 %反射 Rfree 0.1549 2001 0.6 % Rwork 0.1412 333282 - obs 0.1413 335283 93.98 %
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原子変位パラメータ Biso mean : 28.1 Å2 精密化ステップ サイクル : LAST / 解像度 : 1.37→45.27 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 14451 0 107 1682 16240
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.0059 16342 X-RAY DIFFRACTION f_angle_d0.9047 22090 X-RAY DIFFRACTION f_chiral_restr0.0699 2355 X-RAY DIFFRACTION f_plane_restr0.0086 2889 X-RAY DIFFRACTION f_dihedral_angle_d12.8405 6263
LS精密化 シェル 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.37-1.4 0.3802 120 0.3059 18321 X-RAY DIFFRACTION 72.3 1.4-1.44 0.2917 116 0.2724 22969 X-RAY DIFFRACTION 90.52 1.44-1.48 0.2417 155 0.2288 23605 X-RAY DIFFRACTION 93.32 1.48-1.53 0.2561 143 0.1921 23787 X-RAY DIFFRACTION 93.86 1.53-1.59 0.1809 138 0.1753 23933 X-RAY DIFFRACTION 94.56 1.59-1.65 0.1918 144 0.1661 23991 X-RAY DIFFRACTION 94.95 1.65-1.73 0.1836 141 0.1615 24255 X-RAY DIFFRACTION 95.36 1.73-1.82 0.1656 150 0.1612 24254 X-RAY DIFFRACTION 95.78 1.82-1.93 0.1688 141 0.151 24412 X-RAY DIFFRACTION 96.19 1.93-2.08 0.1538 153 0.1432 24394 X-RAY DIFFRACTION 96.63 2.08-2.29 0.1672 144 0.1328 24617 X-RAY DIFFRACTION 97.17 2.29-2.62 0.1518 150 0.1296 24776 X-RAY DIFFRACTION 97.7 2.62-3.3 0.148 152 0.1329 24858 X-RAY DIFFRACTION 98.3 3.3-45.27 0.1237 154 0.1237 25110 X-RAY DIFFRACTION 99.05
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 17) 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 0.927150363234 0.0529343124325 -0.670266325017 0.186388573263 0.0635662247892 1.7793699648 -0.040082328887 0.0441189640931 0.00295907825111 0.0190812428004 -0.00734493373437 0.113618937051 0.0875343154152 -0.198185403789 0.0482474644719 0.185045387987 0.000884556269915 -0.00747009133934 0.175381724528 -0.0059450281984 0.221736178265 -24.6069803628 -1.43572265606 -4.97147961749 2 0.74059107781 0.223009628273 -0.00996488254673 1.42771134878 0.425162086668 0.560157024304 -0.0274937750569 0.0200934298504 0.00188821138457 -0.0423894036471 0.0827057951047 -0.26490011453 -0.0162799039215 0.0709078575271 -0.0390980308929 0.170023261558 0.000399799181635 -0.00652831434379 0.17706468961 -0.00209787095365 0.201377880509 2.46495711878 -11.1497385271 -14.2098837848 3 0.764850946818 0.164206283107 0.257187218693 0.908473410005 0.244504192218 1.11614289663 -0.00647039881332 -0.112733056665 0.0476043263362 0.272720137048 0.0339910366933 -0.048066034609 0.0599899369559 0.0126790668855 -0.0335300531857 0.22791544623 0.00261943356197 -0.0458649606427 0.193872079151 -0.0135754838875 0.214328925729 -0.652570872417 0.793626304367 10.8005284222 4 0.86058207037 -0.260121331904 0.0864049667312 1.00788879689 -0.476807183957 0.838197948522 -0.0113078394682 -0.169048292752 0.103181823544 0.207160870274 0.00641461816495 -0.151961648756 -0.0604131235536 0.110752235049 0.0162892387105 0.225914349122 -0.00768340525815 -0.0550877163799 0.208100296718 -0.0355207558964 0.251673701574 4.39267476264 8.36148946643 7.95680438494 5 0.474813937891 0.200318511238 0.0919927838041 0.929711985839 0.423973120664 0.583775506515 0.0377088287488 -0.000356067820744 0.0367073039342 0.124493938696 0.0520534469152 -0.235426522646 0.0417491149471 0.16268158145 -0.0709900956388 0.164706370547 -0.0013493096733 -0.041494832204 0.168045961812 -0.0204629162022 0.223269664949 5.23226063747 -1.41929250782 -1.57123888629 6 0.762011469046 -0.949776878736 -0.0623049889027 2.22512945482 0.367256257024 0.3647361839 -0.0324684958519 -0.0207914071099 0.0666121909034 0.0457043941109 0.0676911857035 -0.103864932682 -0.011301604351 0.0243862813923 -0.0323732762923 0.154112029101 -0.0132839170795 -0.0146504946685 0.149066590239 -0.00225031136595 0.171128100399 -7.00344787007 1.28879229176 -8.79907418427 7 0.501056094337 -0.0980472477299 -0.0158611546726 1.03842659753 -0.0755227623714 0.930080168112 -0.0244020704905 -0.146012941154 0.02658567165 0.265587694677 0.0261793453942 0.0922003193668 -0.0283729663485 -0.0620095682571 0.00261834947096 0.242877145397 0.00911862968217 0.00802209168903 0.20018696533 -0.0173784296536 0.207300408608 -22.3961858723 4.6049359338 9.41820301357 8 0.651634024753 -0.0342751664233 0.131440884426 0.948937912236 -0.652382304664 1.42424220464 -0.0489471738836 0.0532053186028 0.19257824727 0.0261671011139 -0.0781121166497 -0.190442875638 -0.143844395942 0.215559303714 0.10350311298 0.164495722689 -0.0263188517087 -0.0284339579975 0.166398393955 0.0103445697353 0.236647179696 -14.7832737877 7.70596644666 -30.136180113 9 0.928228070222 -0.284433458049 0.22976888487 0.518872398588 -0.119959413262 0.546017008558 -0.000708911421506 0.115229171252 0.0355812519829 -0.0488774332951 -0.0235703447491 0.093675775657 -0.0127072307731 -0.0433075730424 0.0201968459583 0.14443336656 -0.0110333821751 -0.00790714878669 0.195050790823 -0.00565540448635 0.191504181049 -37.6301716717 -5.74961199713 -40.980870498 10 0.498529795761 -0.131927559365 0.142806328868 0.530247770453 -0.101006014722 0.457608907762 -0.0420716100194 0.124978613325 0.165986616787 -0.0553070604813 0.00182111741588 -0.0313094818835 -0.134909818724 0.0100758442933 0.041077373974 0.196384446966 -0.00555398361183 -0.0178378340494 0.204834885243 0.0306582408326 0.233163941492 -24.259436379 10.5837114472 -38.0477290072 11 1.25784379362 -0.42119904541 0.418554595473 0.600769435164 0.00300311800137 0.707967681713 -0.0208458468234 0.068253294794 0.196393014961 -0.043640689441 -0.027219627239 -0.228475836274 -0.0454953060429 0.137633397655 0.0371430364131 0.144008936797 0.00346554459588 0.0206159577372 0.163638510494 0.000833894751547 0.215947680629 9.72730559997 -27.8267522007 -18.6169088779 12 0.294361266161 -0.0919424430084 -0.036727354297 1.38068919203 -0.496969195144 0.590795403395 -0.0391999627026 -0.0168236565758 -0.0329550867366 0.257741003015 -0.0224187361983 -0.0604579542872 -0.0340455087701 0.0635005040822 0.0579550052304 0.212344762475 -0.00176642288276 -0.00557930695161 0.149861188599 -0.00703804452875 0.15259772312 -8.83099149721 -29.4455165389 2.53736054646 13 0.526901813037 -0.12824093767 0.0131489962774 1.19354209854 -0.188357768774 0.70018967748 -0.0552565062801 -0.098131525026 -0.0951667562422 0.209566427752 0.0245184685278 0.132476594924 0.0821565903481 -0.0273447250802 0.023374080985 0.241664561573 0.00921461516979 0.0531063262515 0.160807939593 0.0115013001199 0.20344233712 -11.6020753782 -40.0967427874 5.1069754986 14 0.449522318908 -0.208576536198 -0.0285846571023 1.0136404572 0.188749946383 0.383770752358 -0.0404328036543 -0.0446549972881 -0.035579667033 0.166397138925 0.0605829849378 -0.253978699651 0.092330328591 0.133578783148 -0.0174512915045 0.16950847278 0.0279898994427 -0.0412297468512 0.159881778887 0.00853329917203 0.214675702084 8.64851109462 -34.382472099 -4.94801334454 15 0.849252758156 0.313323904749 0.353957633057 1.11807144822 0.590342160298 1.52292287156 -0.0501544899313 -0.0582237528334 -0.043969207603 -0.0459736041581 -0.101519589758 0.375680597451 0.166812050171 -0.285725692157 0.0969836525441 0.22990084225 -0.00111624292325 0.00275540793822 0.180094336513 -0.00754368017073 0.294371661895 -18.7275179952 -36.4409182932 -32.4817698805 16 0.592657963241 -0.256823560696 -0.0245189160446 0.659200780944 -0.100260091959 0.588860275256 0.0544140754897 0.236416906825 0.000639557513978 -0.202468576998 -0.0837231306315 -0.133900583749 0.0677950587217 0.0674471693318 0.0248188281332 0.159448139052 0.0197699639209 0.0461696869876 0.231497023854 0.00377455583775 0.14639953169 -5.05227123207 -19.7698252745 -49.9128752889 17 1.36461654741 -0.39738007284 0.395810531094 1.08709320972 -0.205236280064 0.993834027131 0.150678391435 0.299906784712 -0.279595525594 -0.353786892181 -0.0938819417283 0.337909921343 0.221983726333 -0.125114096945 -0.0624495054791 0.329753951153 0.0322213138997 -0.0606280486786 0.28154407416 -0.0749037909281 0.316440166201 -18.6809946405 -40.6143134298 -47.6139734939
精密化 TLSグループ Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (7 x 17) 大きな表を隠す ID Refine TLS-ID Selection details Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 1 chain 'A' and (resid 1 through 57 )AA1 - 57 1 - 57 2 2 chain 'A' and (resid 58 through 88 )AA58 - 88 58 - 88 3 3 chain 'A' and (resid 89 through 159 )AA89 - 159 89 - 159 4 4 chain 'A' and (resid 160 through 228 )AA160 - 228 160 - 228 5 5 chain 'A' and (resid 229 through 285 )AA229 - 285 229 - 285 6 6 chain 'A' and (resid 286 through 331 )AA286 - 331 286 - 331 7 7 chain 'A' and (resid 332 through 456 )AA332 - 456 332 - 456 8 8 chain 'C' and (resid 1 through 57 )CJ1 - 57 1 - 57 9 9 chain 'C' and (resid 58 through 285 )CJ58 - 285 58 - 285 10 10 chain 'C' and (resid 286 through 456 )CJ286 - 456 286 - 456 11 11 chain 'D' and (resid 1 through 47 )DQ1 - 47 1 - 47 12 12 chain '