ソフトウェア | 名称 | バージョン | 分類 |
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XDS | | データ削減 | XSCALE | | データスケーリング | PHENIX | 1.20.1精密化 | PDB_EXTRACT | 3.27 | データ抽出 | 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: apo structure, PDB entry 4trr 解像度: 1.8→22.17 Å / SU ML: 0.1398 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 17.4806 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1779 | 2013 | 2.26 % | 0 |
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Rwork | 0.1461 | 86931 | - | - |
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obs | 0.1468 | 88944 | 99.38 % | - |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 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: 26.81 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.8→22.17 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7311 | 0 | 301 | 738 | 8350 |
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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_d0.0081 | 8000 | X-RAY DIFFRACTION | f_angle_d0.9392 | 10948 | X-RAY DIFFRACTION | f_chiral_restr0.0616 | 1306 | X-RAY DIFFRACTION | f_plane_restr0.0075 | 1525 | X-RAY DIFFRACTION | f_dihedral_angle_d14.3389 | 2925 | | | | | |
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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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1.8-1.85 | 0.2387 | 138 | 0.1934 | 6129 | X-RAY DIFFRACTION | 97.56 | 1.85-1.89 | 0.2136 | 148 | 0.1847 | 6129 | X-RAY DIFFRACTION | 98.34 | 1.89-1.95 | 0.2218 | 140 | 0.1742 | 6190 | X-RAY DIFFRACTION | 98.89 | 1.95-2.01 | 0.198 | 126 | 0.1585 | 6238 | X-RAY DIFFRACTION | 99.59 | 2.01-2.09 | 0.1511 | 132 | 0.1456 | 6181 | X-RAY DIFFRACTION | 99.67 | 2.09-2.17 | 0.1835 | 155 | 0.1369 | 6222 | X-RAY DIFFRACTION | 99.69 | 2.17-2.27 | 0.1811 | 143 | 0.1406 | 6286 | X-RAY DIFFRACTION | 99.64 | 2.27-2.39 | 0.184 | 148 | 0.1453 | 6208 | X-RAY DIFFRACTION | 99.75 | 2.39-2.54 | 0.1832 | 177 | 0.1493 | 6231 | X-RAY DIFFRACTION | 99.97 | 2.54-2.73 | 0.1824 | 148 | 0.1522 | 6238 | X-RAY DIFFRACTION | 100 | 2.73-3.01 | 0.199 | 141 | 0.1525 | 6235 | X-RAY DIFFRACTION | 99.94 | 3.01-3.44 | 0.1987 | 146 | 0.1487 | 6212 | X-RAY DIFFRACTION | 99.91 | 3.44-4.33 | 0.1465 | 135 | 0.1265 | 6252 | X-RAY DIFFRACTION | 99.84 | 4.33-22.17 | 0.1485 | 136 | 0.1393 | 6180 | X-RAY DIFFRACTION | 98.49 |
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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 | 3.70896452203 | 0.699031181316 | -1.52683849679 | 1.96178225951 | -0.18684897557 | 2.72799661543 | 0.131334056815 | 0.401617972507 | 0.268539503959 | -0.247297544045 | 0.0777321052837 | -0.289162415128 | -0.33199838492 | 0.106142178867 | -0.209549962595 | 0.151367492832 | -0.0515578957833 | 0.0567165268486 | 0.179446295492 | 0.00224931143371 | 0.20812395026 | 9.4910434337 | 49.5741981287 | 0.747784396716 | 2 | 3.39393614401 | -0.621848557195 | -2.3568354583 | 3.40882093691 | 2.50121570906 | 6.93535671085 | 0.389077963076 | 0.414513804828 | 0.717117757957 | -0.396842509518 | -0.0117905938817 | -0.0248439379604 | -0.754631363673 | -0.168036547115 | -0.309236643569 | 0.222713896658 | 0.02984835489 | 0.0792414337283 | 0.184996873549 | 0.0887480713613 | 0.336492228891 | -2.55493653163 | 54.1829388103 | -0.0989403754874 | 3 | 1.02034127159 | -0.0580275152251 | 0.470035065714 | 1.82718725996 | 0.162345786764 | 3.19185831687 | 0.100470488934 | -0.0787746279953 | 0.10751351386 | 0.143874398003 | 0.00376798644083 | -0.165317229018 | -0.120290991674 | 0.058332242802 | -0.086073293407 | 0.0857231978979 | -0.0157550861638 | 0.0119472778445 | 0.109654390896 | -0.00163055771451 | 0.158224417544 | -3.01582326355 | 44.5018514412 | 14.8640386534 | 4 | 1.69145723283 | -0.097467031752 | 0.632951926784 | 1.96806537648 | -0.0157461053878 | 3.07175566015 | 0.0937941123831 | 0.0373760341124 | 0.0457741599542 | -0.0578945435824 | -0.0212194161904 | 0.0430989703254 | -0.0286670698814 | 0.00378522020147 | -0.0718347773412 | 0.0699924354923 | 0.00780458633385 | 0.00748066344437 | 0.0689849339909 | -0.00451818906027 | 0.123438491788 | -7.5905517774 | 36.4775994267 | 9.69220112236 | 5 | 2.37398060587 | 0.0230192393935 | 0.4694736779 | 3.03039248897 | 0.0455602954933 | 3.77063224102 | 0.256939066461 | -0.554738130706 | -0.182634418496 | 0.332021880408 | -0.0551742361323 | -0.585476960259 | 0.0422674672152 | 0.378549730544 | -0.17765900293 | 0.127268904483 | -0.044036805149 | -0.0267024693829 | 0.225578224467 | 0.0113732457286 | 0.224066398562 | 6.98938772187 | 33.4532204358 | 14.5851747822 | 6 | 5.77526729153 | 0.780093725386 | -2.54059399485 | 7.51756902801 | -3.93708022303 | 7.12972161843 | 0.276684462859 | -0.851056575471 | 0.342374535103 | 1.01273067435 | -0.241918716448 | -0.680567633343 | -0.396510746944 | 0.949990332267 | -0.0546017549639 | 0.239538438724 | 0.000617531968944 | -0.0714382837463 | 0.316795420869 | -0.0235593179592 | 0.28432876384 | 10.615930168 | 23.3191393216 | 16.9597935192 | 7 | 1.06149218938 | 0.395128179279 | 0.0368411602541 | 1.87658925171 | -0.219014800763 | 1.88878076047 | 0.00326701484946 | 0.000880407623454 | 0.0085224244648 | -0.00844082271288 | 0.00997263860106 | -0.182659756758 | -0.0081022532896 | 0.112071280441 | -0.011095874992 | 0.0797992445253 | 0.0143504392861 | -0.00567374821259 | 0.091736264811 | -0.00650400303629 | 0.139937047071 | -0.372857477534 | 27.3824314022 | 4.3698300815 | 8 | 1.11755649017 | -0.130272852518 | 0.00187466502953 | 1.23591186422 | -0.0815961434899 | 1.44196859798 | 0.0193879195158 | -0.264632611894 | 0.0616078102138 | 0.443874874085 | 0.0192558801251 | 0.147297842493 | -0.134600095384 | -0.118979632198 | -0.0351558399406 | 0.250002890041 | 0.00966621702823 | 0.0590949697808 | 0.173640344407 | -0.0225350322976 | 0.135585961627 | -18.0580619518 | 39.7918723177 | 31.9949163643 | 9 | 4.20584308782 | -0.00675954278728 | 2.40809222078 | 1.12264269272 | -0.296967120935 | 3.47980605226 | -0.161403278535 | 0.0324590726027 | 0.310443360417 | 0.137859286078 | -0.00519230476137 | 0.314134345431 | -0.188111129082 | -0.281214094226 | 0.147885124186 | 0.14942928444 | 0.00146372706222 | 0.0298025751588 | 0.133373693739 | -0.0135848454371 | 0.220414304556 | -26.8370112162 | 29.0836489685 | 21.8054932827 | 10 | 1.02266672454 | 0.683533340966 | -0.329056598875 | 0.65340760848 | 0.239688256986 | 2.25449819538 | 0.126059210843 | -0.267191209306 | -0.221173462113 | 0.851091627762 | -0.278932689001 | 0.294119185714 | 0.99933030901 | -0.275242134419 | 0.167412508298 | 0.571609811231 | -0.147615747702 | 0.173912769275 | 0.267252421934 | 0.00853686687967 | 0.223852717215 | -25.302423915 | -2.30498431567 | 32.8126337793 | 11 | 1.8361035347 | -0.38488202036 | -0.320099764199 | 1.17407461002 | 0.38697368204 | 1.00415780745 | -0.0951681906258 | -0.0989365884125 | -0.0490196506325 | 0.198253043982 | -0.00624121967937 | 0.159865848383 | 0.209630502437 | -0.0977609088984 | 0.0904385859483 | 0.155358185563 | -0.0262769336329 | 0.0226858081746 | 0.114976361464 | 0.00730500888311 | 0.115152410108 | -16.9556081249 | 4.59112584164 | 18.8675562814 | 12 | 4.42923747661 | 0.431858916864 | 0.557729449032 | 2.7996198637 | 0.353162567004 | 3.11692697637 | -0.110996239722 | -0.233576153993 | -0.364254566787 | 0.542512999156 | -0.047374166755 | -0.24089193012 | 0.184646250189 | 0.313192006972 | 0.142633012166 | 0.289292218073 | -0.0143843209652 | 0.0323865193241 | 0.162592215399 | 0.0442950853104 | 0.162725226388 | -13.0062546081 | 9.06748570388 | 30.3982576504 | 13 | 4.02456629157 | -2.35733136404 | -0.328499730189 | 5.91122741073 | -0.757997279515 | 1.88037364245 | -0.391734385826 | -0.760950970254 | -0.528575034296 | 0.42145509874 | -0.201591305058 | -1.29284881912 | 0.541358359886 | 0.87055838557 | 0.38730466106 | 0.400616765282 | 0.0890341649856 | -0.06211720275 | 0.437504484556 | 0.154480725775 | 0.422931030811 | 1.28794305419 | 12.7381337132 | 35.6651022008 | 14 | 3.090267318 | 0.565806145152 | 0.611208266217 | 1.87838331326 | -0.281072195171 | 2.09158796224 | 0.0260855821316 | -0.235585918286 | 0.0835062058735 | 0.340632929659 | -0.050104815277 | 0.113283825983 | 0.215753604136 | -0.0944282141924 | 0.0246002385818 | 0.195282382818 | -0.00813993537329 | 0.0173680675602 | 0.0937210165181 | -0.0227997942412 | 0.127857882633 | -18.0729848039 | 16.9961634112 | 29.1094105553 | 15 | 2.33669125698 | -0.451680849887 | -0.441447795284 | 1.89019208048 | -0.456681573039 | 3.34981095165 | -0.0452610668282 | 0.476215563834 | 0.0276573598343 | -0.56753473964 | -0.0283195791757 | -0.112546037974 | 0.069461141465 | -0.00129840174806 | 0.0570527274497 | 0.227870120258 | 0.0151846241413 | 0.0129600716454 | 0.21170464595 | 0.00128583833531 | 0.0938932753984 | -1.34920484731 | 6.00806632983 | -11.49324497 | 16 | 1.45038248072 | 0.142381357924 | -0.306956125902 | 1.6381638623 | 0.213032804579 | 1.03289796514 | -0.0278552714717 | 0.132250094623 | 0.0298294784689 | -0.122015192357 | -0.0224045409789 | 0.0496729694568 | 0.0880111689769 | -0.0553485600923 | 0.0350822041016 | 0.112986923337 | 0.00858022353523 | -0.0159374651572 | 0.103668903244 | 0.00861216453112 | 0.0814629738379 | -8.38724146402 | 7.36512045044 | 2.55346911609 | 17 | 2.58296856361 | -1.23404976318 | 0.157606245495 | 2.31685546046 | -0.0485923355693 | 2.56972777556 | 0.0637854056338 | 0.170621334881 | 0.0405391956377 | -0.17872327413 | -0.0730926259923 | 0.104421369449 | 0.120209521453 | -0.145112475273 | -0.00164458866667 | 0.119815281772 | -0.0195015747778 | -0.0150231919461 | 0.0774929799929 | 0.008482637495 | 0.111450177327 | -8.55803286663 | 22.1874261631 | -0.407109002886 | 18 | 4.67344447285 | 0.343748792897 | 2.43502210812 | 3.53643568326 | -1.66641106614 | 5.2491714242 | 0.0577154088856 | 0.588852466445 | -0.225262204559 | -0.529131042354 | 0.202984009689 | -0.24333230576 | 0.219413303202 | 0.133298463845 | -0.282234742126 | 0.185395856165 | -0.0272616330676 | 0.0738052240958 | 0.19265094718 | -0.0208137660582 | 0.181113741015 | 2.92953004969 | 41.5650217501 | -3.55132804447 | 19 | 2.82007861563 | 0.246071935411 | -0.83527271864 | 1.78851250376 | -0.216538104982 | 2.51433566312 | 0.116999683648 | -0.00812486891835 | 0.031166390492 | -0.158611905408 | 0.0489740332185 | -0.243263962151 | -0.0738030976326 | 0.0650203847202 | -0.17269385721 | 0.113122816533 | -0.0207636201341 | 0.0495240472269 | 0.149900392278 | -0.0111447283436 | 0.19649812175 | 8.23672886284 | 41.6589217031 | 0.743122262892 |
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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 'B' and (resid 40 through 66 )BG40 - 66 | 38 - 64 | 2 | 2 | chain 'B' and (resid 67 through 81 )BG67 - 81 | 65 - 79 | 3 | 3 | chain 'B' and (resid 82 through 129 )BG82 - 129 | 80 - 127 | 4 | 4 | chain 'B' and (resid 130 through 177 )BG130 - 177 | 128 - 175 | 5 | 5 | chain 'B' and (resid 178 through 214 )BG178 - 214 | 176 - 204 | 6 | 6 | chain 'B' and (resid 215 through 228 )BG215 - 228 | 205 - 218 | 7 | 7 | chain 'B' and (resid 229 through 261 )BG229 - 261 | 219 - 251 | 8 | 8 | chain 'C' and (resid 3 through 177 )CL3 - 177 | 1 - 175 | 9 | 9 | chain 'C' and (resid 178 through 261 )CL178 - 261 | 176 - 259 | 10 | 10 | chain 'D' and (resid 3 through 81 )DQ3 - 81 | 1 - 79 | 11 | 11 | chain 'D' and (resid 82 through 177 )DQ82 - 177 | 80 - 175 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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