ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | dev_3885精密化 | PDB_EXTRACT | 3.25 | データ抽出 | XDS | | データ削減 | XSCALE | | 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: 5MAU 解像度: 1.51→36.34 Å / SU ML: 0.2438 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 25.654 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 | 0.1926 | 1575 | 2.34 % |
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Rwork | 0.1749 | 65798 | - |
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obs | 0.1754 | 67373 | 98.3 % |
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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: 33.82 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.51→36.34 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2994 | 0 | 136 | 406 | 3536 |
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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_d0.0182 | 3288 | X-RAY DIFFRACTION | f_angle_d1.7264 | 4480 | X-RAY DIFFRACTION | f_chiral_restr0.1022 | 453 | X-RAY DIFFRACTION | f_plane_restr0.0166 | 572 | X-RAY DIFFRACTION | f_dihedral_angle_d22.2567 | 458 | | | | | |
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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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1.51-1.56 | 0.372 | 118 | 0.3911 | 5034 | X-RAY DIFFRACTION | 83.2 | 1.56-1.61 | 0.3352 | 150 | 0.3455 | 6029 | X-RAY DIFFRACTION | 99.29 | 1.61-1.68 | 0.3571 | 138 | 0.314 | 6045 | X-RAY DIFFRACTION | 99.84 | 1.68-1.76 | 0.3131 | 150 | 0.293 | 6046 | X-RAY DIFFRACTION | 99.9 | 1.76-1.85 | 0.2963 | 151 | 0.2504 | 6039 | X-RAY DIFFRACTION | 99.66 | 1.85-1.96 | 0.2557 | 138 | 0.207 | 6087 | X-RAY DIFFRACTION | 99.94 | 1.96-2.12 | 0.2101 | 149 | 0.1735 | 6069 | X-RAY DIFFRACTION | 99.94 | 2.12-2.33 | 0.197 | 142 | 0.1653 | 6053 | X-RAY DIFFRACTION | 99.84 | 2.33-2.67 | 0.1972 | 144 | 0.1656 | 6102 | X-RAY DIFFRACTION | 99.89 | 2.67-3.36 | 0.171 | 151 | 0.1626 | 6118 | X-RAY DIFFRACTION | 99.94 | 3.36-36.34 | 0.1479 | 144 | 0.1386 | 6176 | X-RAY DIFFRACTION | 99.76 |
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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 | 0.532180143175 | -0.218273743969 | -0.369234496316 | 0.178888332352 | 0.251291643817 | 0.368217122826 | 0.0264124583873 | -0.318055923967 | -0.17763850178 | 0.136688006484 | -0.171826401302 | -0.175942534495 | 0.747659067577 | -0.0813581293997 | -0.00306094930221 | 0.386372117384 | -0.0778594820296 | -0.00543882223334 | 0.164782431613 | 0.0359096530013 | 0.255775942524 | 5.33863806654 | -9.27539149662 | 2.84156374277 | 2 | 0.445041591223 | 0.0542472015197 | -0.0464904466953 | 0.142017215675 | -0.037224797023 | 0.394634325898 | -0.285952281418 | 0.271182291052 | 0.127490704182 | -0.486951112098 | 0.288793216663 | 0.209084603698 | 0.0563899730597 | -0.444247260562 | 0.0023232383603 | 0.36446482426 | -0.105010536941 | -0.0245442802247 | 0.269573805559 | 0.0447732601013 | 0.251300199457 | -3.50432539804 | -2.72074227802 | -9.4934889388 | 3 | 0.489128724784 | -0.234438256746 | 0.023099315314 | 0.128728299788 | -0.0433942282064 | 0.168308737813 | 0.0876059605936 | 0.385118821358 | -0.052552877549 | -0.0204011839847 | 0.0161447032358 | 0.0215037058717 | 0.186839701245 | -0.110961025159 | 0.013180687828 | 0.34007577177 | -0.071158094499 | -0.00633766759414 | 0.170153479213 | 0.0218039466587 | 0.222848103106 | 3.30514172576 | -1.19260914609 | -9.42301049676 | 4 | 0.309245188361 | -0.176684549882 | 0.35370367536 | 0.209165502792 | -0.381499940398 | 0.701062562209 | -0.131542753246 | 0.574158890322 | -0.734701834349 | -0.421090075132 | -0.476140106854 | -0.600537576167 | 0.685203097061 | 0.270128848008 | 0.0358599348145 | 0.453041108142 | 0.0121224961227 | 0.115581028929 | 0.412432073181 | -0.0157035778084 | 0.48569557005 | 8.36706499558 | -12.9461047243 | -6.72423405667 | 5 | 0.661876878019 | 0.270723651923 | 0.12332702732 | 0.423314498025 | -0.273698735779 | 0.365961511046 | 0.0198200154524 | -0.265037829788 | -0.127859172536 | -0.265730859835 | -0.0276029004328 | 0.0267454249406 | -0.116681322398 | -0.141565596111 | 2.33160927807E-5 | 0.251859333575 | 0.0120081131221 | 0.00408778698686 | 0.263251189447 | 0.0104727184998 | 0.198071318509 | 8.74657493615 | -0.420596970838 | 7.61126068114 | 6 | 0.126239706834 | -0.0391886685637 | -0.149850587469 | 0.333204769442 | 0.160317919784 | 0.191194189187 | 0.0889238263389 | -0.380916137916 | -0.11857005598 | 0.122553551021 | 0.0899654633888 | -0.0572740833935 | 0.065565959733 | -0.112066871499 | 5.14407899783E-5 | 0.261931829394 | -0.0394426421079 | 0.0182929056795 | 0.515792307396 | 0.0589075083877 | 0.279158298728 | -6.87124494236 | 2.27611110059 | 13.6338032051 | 7 | 1.12328029784 | 0.270030126988 | 0.475163466457 | 1.44581152354 | 0.128237857003 | 1.7838681014 | -0.065459742675 | -0.170295449356 | 0.138047463872 | 0.00722837448921 | 0.0285373360678 | 0.0384638432707 | -0.0895375283715 | -0.141572561697 | 4.63930477716E-5 | 0.191288403745 | 0.0188321729964 | 0.0102735076395 | 0.16065355962 | -0.00924455164124 | 0.197584715748 | 6.26257472661 | 8.05238800344 | 6.6916249458 | 8 | 0.122219093125 | -0.17542894762 | 0.0324455941262 | 0.377685563042 | -0.0528428130695 | 0.23460223153 | -0.111844239253 | -0.230486009838 | -0.0124504872909 | 0.000598519020494 | 0.0823114190812 | 0.289363802519 | -0.144569906848 | -0.352932634368 | 8.30650022848E-5 | 0.253194238664 | 0.038015561239 | -0.035673101794 | 0.227566521463 | 0.0129435972995 | 0.355053222674 | -6.02389082805 | 13.3827079479 | 0.872656687963 | 9 | 0.317997342526 | -0.262697395857 | -0.223511203101 | 0.528532121468 | -0.0842270131434 | 1.30690907456 | -0.0100431786227 | -0.131578663884 | 0.121061647325 | -0.0350278577456 | -0.00268439606545 | 0.0715034081779 | -0.0261272264467 | -0.198366391006 | 1.72638456387E-5 | 0.228844253436 | -0.0185985279446 | 9.62194790014E-5 | 0.177635936837 | 0.0252329436876 | 0.238347946271 | 3.39333873861 | 7.82194091525 | -2.31153674327 | 10 | 0.2149931034 | 0.122436014975 | 0.0506793342931 | 0.197000961809 | 0.206090447996 | 0.243152739977 | 0.237359974048 | 0.375986685951 | -0.244052430856 | -0.302561938837 | 0.0430075361981 | -0.144889055091 | 0.183093868682 | 0.134075790604 | -0.000221714402139 | 0.347356403389 | 0.0467441366477 | 0.0175661696741 | 0.328116304278 | 0.0340079603779 | 0.297015988163 | 27.3222631147 | -9.54129890467 | 8.59405291361 | 11 | 0.606269261169 | 0.765743755129 | 0.579522338512 | 1.10457614406 | 0.459909973452 | 1.27902089326 | 0.460792975434 | -0.188179345786 | -0.899373599188 | 0.0389185977506 | 0.244255491417 | -0.497980557426 | 0.715459637772 | 0.244068806628 | 0.41146978282 | 0.48828397749 | 0.0772503930469 | -0.0878654966721 | 0.296575009247 | 0.257639267349 | 0.469040993421 | 32.5388933557 | -17.379352161 | 20.2624288708 | 12 | 0.00963254974221 | 0.025095319648 | -0.0171592726081 | 0.0475912069657 | -0.038268322084 | 0.026889181246 | 0.438820314329 | 0.416266707253 | -0.563585471124 | -0.380828897753 | 0.340720258801 | 0.279867081179 | 0.806295581047 | -0.246256780764 | -5.84657747013E-5 | 0.888251862958 | 0.0247352208769 | -0.164712084113 | 0.42065746892 | -0.0291455924361 | 0.896948933204 | 27.3082217467 | -20.3233435081 | 7.48377382861 | 13 | 0.779077234369 | 0.139953362885 | 0.123119846521 | 0.175924865814 | -0.262512445322 | 0.542373180748 | -0.00708217493974 | -0.301288796755 | -0.208001266503 | 0.0709628791044 | -0.0229334261994 | -0.170904619666 | 0.352198978122 | -0.108364764897 | -0.000122465574508 | 0.282069909638 | 0.0019031136491 | 0.00826967691158 | 0.197626341352 | 0.0434198378357 | 0.247779723914 | 21.276957225 | -3.14340031517 | 14.5593255261 | 14 | 0.576235678247 | -0.315990162302 | 0.363343051163 | 0.409534550046 | 0.293673311926 | 1.02540975123 | 0.0180627134466 | -0.277393113209 | 0.20062881213 | -0.122581002926 | -0.111788475649 | -0.148795880741 | -0.0707737955631 | 0.12865113565 | -2.38765834527E-5 | 0.234156428068 | -0.0184691127675 | -0.0190001009481 | 0.302863169122 | 0.047796719311 | 0.300018259063 | 32.0900928145 | 2.52513362044 | 19.3065115496 | 15 | 0.236934825343 | -0.19966311274 | 0.0711608601628 | 0.227629053169 | 0.0343337141761 | 0.132973288123 | -0.0806200935163 | -0.78285703928 | -0.0122635099433 | 0.190966440894 | 0.0672525116684 | 0.280876835747 | 0.122247502308 | -0.659667953745 | -0.00154245046117 | 0.251080222492 | 0.0043978336061 | 0.0320201166874 | 0.519238416243 | 0.0128129791049 | 0.232730473562 | 10.840474921 | 2.44156126029 | 25.6520077246 | 16 | 0.127423373192 | 0.0891621659618 | 0.00760100082059 | 0.16745168995 | -0.121313896104 | 0.143234721988 | 0.108364277407 | -0.546972077561 | 0.411203228934 | 0.122788507107 | -0.268045873256 | -5.28812475113E-5 | -0.564209815947 | -0.352783130254 | -0.000409637851342 | 0.33022181695 | 0.0463755233381 | -0.0151453268343 | 0.434132304783 | -0.0749620634184 | 0.277558955081 | 24.2987051896 | 7.77881768547 | 29.9422475237 | 17 | 0.821981946794 | -0.58131238767 | 0.402723621255 | 0.83085590666 | -0.34654323083 | 1.23286417452 | 0.0129667579938 | -0.473794836792 | -0.0566164469703 | 0.0733686978525 | -0.0594540226259 | -0.10167605666 | 0.104383084064 | -0.0288144878542 | -1.41117525638E-5 | 0.235932318623 | -0.0326302882139 | -0.00464835395241 | 0.307474796462 | 0.0666176257302 | 0.218745303542 | 28.3992199203 | -3.30919042629 | 23.7524993052 | 18 | 0.329313958537 | 0.130528923596 | 0.478690588671 | 0.881781458852 | 0.2323213149 | 0.653097892732 | 0.140762734375 | -0.468205702584 | -0.147821872342 | 0.146821790677 | -0.0768675763461 | -0.145471494229 | 0.338485515352 | 0.0411366282815 | -3.1473173232E-5 | 0.295455788672 | -0.0253242862335 | -0.00608951216437 | 0.414843374477 | 0.127417228649 | 0.287928927154 | 26.8230649201 | -9.04888203008 | 25.8213894282 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION ID | Refine TLS-ID | Selection details | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 1 through 10 )AA1 - 10 | 1 - 10 | 2 | 2 | chain 'A' and (resid 11 through 21 )AA11 - 21 | 11 - 21 | 3 | 3 | chain 'A' and (resid 22 through 37 )AA22 - 37 | 22 - 37 | 4 | 4 | chain 'A' and (resid 38 through 49 )AA38 - 49 | 38 - 49 | 5 | 5 | chain 'A' and (resid 50 through 63 )AA50 - 63 | 50 - 63 | 6 | 6 | chain 'A' and (resid 64 through 83 )AA64 - 83 | 64 - 89 | 7 | 7 | chain 'A' and (resid 84 through 148 )AA84 - 148 | 90 - 160 | 8 | 8 | chain 'A' and (resid 149 through 165 )AA149 - 165 | 161 - 180 | 9 | 9 | chain 'A' and (resid 166 through 182 )AA166 - 182 | 181 - 197 | 10 | 10 | chain 'B' and (resid 1 through 10 )BH1 - 10 | 1 - 10 | 11 | 11 | chain 'B' and (resid 11 through 37 )BH11 - 37 | 11 - 37 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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