ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.10_2155精密化 | PDB_EXTRACT | 3.27 | データ抽出 | XDS | | データ削減 | Aimless | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 1DFB 解像度: 1.70000520394→44.7076752723 Å / SU ML: 0.224743460608 / 交差検証法: THROUGHOUT / σ(F): 1.34454775085 / 位相誤差: 22.9834555405 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 |
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Rfree | 0.221877027097 | 1998 | 3.63808517999 % |
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Rwork | 0.179349882926 | 52921 | - |
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obs | 0.180877855087 | 54919 | 96.5778598435 % |
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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 |
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原子変位パラメータ | Biso mean: 38.1791563834 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.70000520394→44.7076752723 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3394 | 0 | 12 | 341 | 3747 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.0101717588849 | 3505 | X-RAY DIFFRACTION | f_angle_d1.06362218998 | 4776 | X-RAY DIFFRACTION | f_chiral_restr0.0622099096331 | 541 | X-RAY DIFFRACTION | f_plane_restr0.00680947514659 | 610 | X-RAY DIFFRACTION | f_dihedral_angle_d14.3758118642 | 1267 | | | | | |
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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 (%) |
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1.70000520394-1.7425 | 0.39464991286 | 111 | 0.353556494514 | 2930 | X-RAY DIFFRACTION | 75.4403373853 | 1.7425-1.7896 | 0.362193146933 | 121 | 0.309046787515 | 3219 | X-RAY DIFFRACTION | 83.688298672 | 1.7896-1.8423 | 0.308305854741 | 135 | 0.268791050586 | 3560 | X-RAY DIFFRACTION | 92.8858722976 | 1.8423-1.9018 | 0.278481816211 | 146 | 0.23631145236 | 3872 | X-RAY DIFFRACTION | 99.7765085672 | 1.9018-1.9697 | 0.284472761377 | 145 | 0.228589679803 | 3857 | X-RAY DIFFRACTION | 99.8752183679 | 1.9697-2.0486 | 0.223166654183 | 146 | 0.174418212026 | 3880 | X-RAY DIFFRACTION | 99.9751676186 | 2.0486-2.1418 | 0.213433461752 | 148 | 0.177983051754 | 3881 | X-RAY DIFFRACTION | 99.95038452 | 2.1418-2.2547 | 0.232551976425 | 146 | 0.182564786328 | 3874 | X-RAY DIFFRACTION | 99.9751305645 | 2.2547-2.396 | 0.20201774822 | 147 | 0.175670041138 | 3899 | X-RAY DIFFRACTION | 99.9505928854 | 2.396-2.581 | 0.237800989882 | 146 | 0.17999481004 | 3901 | X-RAY DIFFRACTION | 100 | 2.581-2.8407 | 0.25084099298 | 149 | 0.180173424458 | 3935 | X-RAY DIFFRACTION | 99.9755201958 | 2.8407-3.2516 | 0.210013850509 | 150 | 0.175286461353 | 3950 | X-RAY DIFFRACTION | 100 | 3.2516-4.0963 | 0.194552433658 | 150 | 0.158425681166 | 3979 | X-RAY DIFFRACTION | 100 | 4.0963-44.7076 | 0.193384770967 | 158 | 0.156144098928 | 4184 | X-RAY DIFFRACTION | 100 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION 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) |
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1 | 4.91092814281 | -2.47149993074 | 1.58782654842 | 5.07388020953 | -2.01455040313 | 5.73884984062 | 0.0101002598943 | -0.134187919173 | -0.482842362692 | 0.0649331780048 | 0.210020161883 | 0.433103358475 | 0.129853707288 | -0.367071195385 | -0.36600015816 | 0.148536445154 | 0.0500413221988 | 0.058789390456 | 0.178552869804 | 0.0190698424716 | 0.189289847159 | 24.3609986668 | 43.6014435563 | 51.6249875229 | 2 | 3.22397996048 | -0.561163120185 | 0.244046841952 | 2.35474631221 | -0.486898188236 | 2.94101191806 | -0.12720563205 | -0.513038783243 | -0.00211666471415 | 0.301782817514 | 0.140667637512 | 0.211012093226 | -0.124117453952 | -0.190121160552 | -0.0353396917788 | 0.337044061815 | 0.1432011696 | 0.0764964238119 | 0.286698179162 | 0.022802699704 | 0.205722047891 | 28.1982091049 | 47.6958164352 | 60.4861901095 | 3 | 4.62793908721 | -0.957709012672 | 2.1790425842 | 2.27602669352 | -1.86270427312 | 2.05334240528 | -0.148450093024 | -0.770151746384 | -0.21946019357 | 0.575572613568 | 0.198214499061 | 0.215623304152 | -0.0807252544677 | -0.0381643440528 | 0.295114317302 | 0.390868714351 | 0.154048213472 | 0.0769901608894 | 0.335621651381 | 0.0415940779583 | 0.180897337121 | 35.094116606 | 43.4264146777 | 62.2256459207 | 4 | 3.93887934238 | -1.25233469038 | 0.042372490118 | 1.86593956183 | -0.163807713231 | 5.25402633947 | 0.089842377302 | -0.849202470065 | 0.178500170577 | 0.387612889117 | 0.171506549695 | -0.212784421819 | -0.378128007382 | 0.0665779867072 | 0.0489694539947 | 0.412515986995 | 0.138192762427 | 0.0616929864731 | 0.441408671672 | 0.0267555624796 | 0.221286201236 | 39.1685628331 | 44.3815507922 | 67.3744753486 | 5 | 0.470832346738 | 0.491567909812 | -0.409256021869 | 0.515593910387 | -0.167553315665 | 2.29835217495 | -0.212772416619 | 0.0425368757425 | 0.0127419606965 | 0.385554550354 | 0.0740390822872 | 0.239368169766 | -0.0500344807984 | -0.205131067344 | 0.149429224866 | 0.194615396362 | 0.0754568151948 | 0.026778446565 | 0.220237965227 | 0.00542215521795 | 0.26153878165 | 24.3144395632 | 48.1840099935 | 40.9143653682 | 6 | 2.21286241078 | -0.613445406092 | -0.748803424074 | 3.14948231159 | 0.285821281217 | 2.81455707116 | -0.0602661062606 | 0.124919144158 | -0.0485903257818 | -0.219178152513 | 0.0596963519257 | -0.0927282644805 | 0.162547173288 | -0.0534356713382 | -0.00559001934859 | 0.0867248145568 | -0.0232052437085 | 0.0116101960777 | 0.133792468734 | -0.00789557477468 | 0.160790252229 | 32.2827396601 | 40.2087540766 | 25.4904373899 | 7 | 1.49385502619 | 0.990388818379 | 1.47883808513 | 2.10746012829 | 0.905553170688 | 1.74096725897 | -0.0533887489114 | 0.294343568895 | -0.193921952948 | -0.382183011008 | 0.120525838873 | 0.118224283464 | 0.165088810522 | -0.170416236139 | 0.473861746127 | 0.25260791668 | -0.0568423609496 | 0.0534374300622 | 0.205315978133 | 0.0100319220898 | 0.234566024202 | 26.6949641284 | 33.8070275076 | 23.4000407237 | 8 | 0.739402021143 | -0.655939647893 | 0.607639571795 | 1.65948847298 | 1.7513814344 | 8.68125010797 | -0.0261415043148 | 0.561319692343 | -0.305057084773 | -0.5436731529 | -0.00933303989281 | 0.376204001156 | -0.403938996423 | -0.121195019689 | -0.101363509077 | 0.328671947701 | -0.0722613785956 | -0.0446655678936 | 0.396241051598 | -0.0685243201905 | 0.285230569429 | 25.9000618462 | 37.2221525706 | 12.9410261602 | 9 | 5.01260753601 | -3.58239519074 | -3.40302001255 | 3.51511719847 | 3.26185576594 | 3.54061785405 | -0.0398651127413 | -0.016308096433 | 0.318823797574 | 0.300297566415 | 0.0661903909116 | -0.442273373048 | -0.364766009893 | 0.320649794347 | -0.256620841903 | 0.292762154128 | 0.00323529434725 | -0.0113981665458 | 0.201827755784 | 0.0200563585356 | 0.247120674887 | 55.8207450716 | 44.8778418551 | 49.5596727389 | 10 | 6.71525648764 | 5.39555805548 | -4.17192657555 | 5.21117321559 | -4.4855119856 | 4.23752151829 | -0.127181262187 | -0.688802600598 | 0.564121322204 | 0.604547675035 | 0.0437843053684 | -0.200000756624 | -1.07763817273 | 0.35013018459 | -0.111318311325 | 0.5032205195 | 0.104354692437 | -0.112784952278 | 0.348217066642 | -0.133961198998 | 0.231143814759 | 53.2442791016 | 49.0483930134 | 71.071071085 | 11 | 4.89017357475 | -0.247229764216 | 4.42106804966 | 1.55498492852 | -1.03339968333 | 4.48756925719 | 0.0072982238883 | 0.0514317450357 | -0.32239848624 | 0.115080958063 | 0.130345717485 | 0.11411199232 | 0.024786738099 | -0.085288639294 | -0.234287922033 | 0.228719617604 | 0.0711283918422 | 0.0190582874886 | 0.204519816207 | -0.0184907467761 | 0.166989394418 | 44.4440202424 | 39.0172919342 | 53.7524772991 | 12 | 3.96659615782 | -0.323009465119 | -1.12254947338 | 4.43286234058 | 1.13334427369 | 4.91204572064 | -0.28453793997 | -0.329273497288 | 0.0275041631368 | 0.322036164567 | 0.184829263339 | -0.184684563464 | -0.122837124339 | 0.280894717152 | 0.107920610781 | 0.221103441312 | 0.0756850496622 | -0.0608581034387 | 0.211139944573 | 0.00560554178786 | 0.18953198485 | 53.9582570426 | 38.1380588552 | 60.3448474249 | 13 | 1.35785764108 | -0.392058938204 | 0.606798938153 | 1.26604402713 | -0.907924123749 | 3.03260584701 | 0.0920982715392 | 0.0567940008094 | 0.160090198879 | 0.12645141507 | -0.0448644449791 | -0.303288242279 | -0.181118682279 | -0.0912865703456 | -0.0578763342012 | 0.154437150397 | 0.056614935202 | 0.011206311608 | 0.165612136509 | -0.00320542271706 | 0.187308430811 | 49.4582199835 | 42.4709815099 | 49.4595790751 | 14 | 2.26224274957 | 1.5280600301 | 0.902285355882 | 2.19341733782 | -0.438041685185 | 4.89534204792 | -0.0256956448681 | 0.622427628715 | -0.0197409524826 | -0.412686721991 | 0.1072514618 | 0.426086641723 | 0.348568212723 | -0.466713714057 | -0.188688384289 | 0.148825926173 | -0.0549443531679 | -0.0302506579958 | 0.273424137263 | 0.0115040952106 | 0.222348123289 | 32.4962427895 | 46.6230492783 | 15.0122482677 | 15 | 4.61450475482 | -4.49777195875 | 4.49773316787 | 6.18001285352 | -4.44435029356 | 5.38121683827 | -0.234072459376 | -0.173466248239 | 0.0968289834961 | -0.0405480669605 | 0.00242637049443 | -0.311387996494 | -0.0370911905263 | 0.268087054609 | 0.226269200141 | 0.0857424644745 | 0.0067412748145 | 0.0544374834021 | 0.192078270018 | -0.0175109418648 | 0.127210086945 | 45.1739495176 | 48.0023750028 | 23.452956824 | 16 | 1.54961608455 | 0.546736082808 | 0.0601942168835 | 9.08680484775 | -6.23678765267 | 4.41881755284 | -0.0285312500205 | 0.0343142334304 | 0.208186695622 | -0.14738333835 | -0.0131533367465 | 0.024974634844 | -0.15584587277 | 0.359333315658 | 0.175333985768 | 0.239961169359 | -0.0434810789337 | 0.00843121750967 | 0.21425389134 | -0.0229256143036 | 0.274451134647 | 41.6453724924 | 56.4768836728 | 21.7177158868 | 17 | 3.51940164677 | -2.63220966899 | 3.25129509427 | 4.41891321628 | -4.36915556165 | 7.83467554231 | -0.0696140798821 | -0.023687291019 | -0.0302588494287 | -0.231901225157 | 0.171221057872 | 0.114032443278 | 0.0646670961401 | 0.0469514883639 | -0.0786673220552 | 0.109524482901 | -0.031409362582 | 0.011467097694 | 0.105656984697 | -0.0321213706094 | 0.153499956709 | 40.9248466026 | 48.6008987158 | 21.2874446224 | 18 | 7.95607470671 | -2.41556707558 | 3.84500131345 | 3.94797600125 | -1.69170839977 | 4.7018564738 | 0.00473385414148 | 0.453871494564 | 0.164801237643 | -0.685381734803 | -0.326515733671 | -0.253537167924 | 0.0872682482475 | 1.20630709798 | -0.261585478313 | 0.0792524297552 | 0.00999000202 | 0.140231704916 | 0.421819681499 | 0.0300782427662 | 0.151461083754 | 48.3038138419 | 48.0739474257 | 14.3226351324 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'H' and (resid 1 through 17 )2 | X-RAY DIFFRACTION | 2 | chain 'H' and (resid 18 through 87 )3 | X-RAY DIFFRACTION | 3 | chain 'H' and (resid 88 through 99 )4 | X-RAY DIFFRACTION | 4 | chain 'H' and (resid 100 through 103 )5 | X-RAY DIFFRACTION | 5 | chain 'H' and (resid 104 through 119 )6 | X-RAY DIFFRACTION | 6 | chain 'H' and (resid 120 through 188 )7 | X-RAY DIFFRACTION | 7 | chain 'H' and (resid 189 through 203 )8 | X-RAY DIFFRACTION | 8 | chain 'H' and (resid 204 through 220 )9 | X-RAY DIFFRACTION | 9 | chain 'L' and (resid 3 through 25 )10 | X-RAY DIFFRACTION | 10 | chain 'L' and (resid 26 through 32 )11 | X-RAY DIFFRACTION | 11 | chain 'L' and (resid 33 through 48 )12 | X-RAY DIFFRACTION | 12 | chain 'L' and (resid 49 through 75 )13 | X-RAY DIFFRACTION | 13 | chain 'L' and (resid 76 through 113 )14 | X-RAY DIFFRACTION | 14 | chain 'L' and (resid 114 through 128 )15 | X-RAY DIFFRACTION | 15 | chain 'L' and (resid 129 through 150 )16 | X-RAY DIFFRACTION | 16 | chain 'L' | | | | | | | | | | | | | | | |
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