ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.20.1_4487精密化 | Aimless | | データスケーリング | XDS | | データ削減 | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.85→48.3 Å / SU ML: 0.2605 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.5264 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 | 0.2401 | 1037 | 5.16 % |
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Rwork | 0.2026 | 19049 | - |
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obs | 0.2046 | 20086 | 99.21 % |
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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: 45.13 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.85→48.3 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1676 | 0 | 68 | 104 | 1848 |
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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_d0.0059 | 1789 | X-RAY DIFFRACTION | f_angle_d0.831 | 2397 | X-RAY DIFFRACTION | f_chiral_restr0.052 | 266 | X-RAY DIFFRACTION | f_plane_restr0.0054 | 308 | X-RAY DIFFRACTION | f_dihedral_angle_d14.0529 | 648 | | | | | |
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Refine LS restraints NCS | タイプ: Torsion NCS / Rms dev position: 0.704409991423 Å |
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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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1.85-1.95 | 0.3974 | 144 | 0.3476 | 2687 | X-RAY DIFFRACTION | 99.3 | 1.95-2.07 | 0.3276 | 163 | 0.2645 | 2657 | X-RAY DIFFRACTION | 99.44 | 2.07-2.23 | 0.2575 | 126 | 0.2332 | 2717 | X-RAY DIFFRACTION | 99.13 | 2.23-2.45 | 0.3017 | 134 | 0.2267 | 2702 | X-RAY DIFFRACTION | 99.23 | 2.45-2.81 | 0.268 | 161 | 0.2305 | 2727 | X-RAY DIFFRACTION | 99.48 | 2.81-3.54 | 0.2293 | 139 | 0.2012 | 2723 | X-RAY DIFFRACTION | 98.72 | 3.54-48.3 | 0.202 | 170 | 0.1649 | 2836 | X-RAY DIFFRACTION | 99.24 |
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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 | 9.44646332464 | 1.04173437783 | 1.3798495634 | 2.19292427207 | 1.71815779435 | 2.27338644083 | -0.158187367558 | -0.0707225613874 | 0.541383778752 | -0.870120228727 | 0.0987466620495 | 0.547508522681 | -1.79630819939 | 0.180183770204 | -0.0261416194718 | 0.533499237209 | -0.0048993869254 | 0.0217450051724 | 0.372242937809 | 0.0768565990295 | 0.339420815844 | 13.2290554405 | 32.3518369247 | -13.3584187363 | 2 | 8.67753131988 | -3.67735782036 | 3.13413729331 | 6.01601556453 | -6.56658595602 | 9.53699833514 | 0.515982649371 | 0.191237279866 | -0.716146215742 | -0.16199919803 | -0.459495311618 | -0.0417431249893 | 1.53602762461 | 0.725592592511 | -0.117485156619 | 0.461081675069 | 0.0752987795185 | -0.0139504305897 | 0.341559919297 | -0.0290236693763 | 0.282448531446 | 11.9096482577 | 12.7498769008 | -26.4081763337 | 3 | 7.6304340995 | 5.35801338061 | 5.24013599603 | 5.86609245154 | 4.92414873076 | 4.36523841852 | -0.00411877257954 | 0.254586292363 | -0.0799989450652 | 0.781238603668 | 0.0522722172047 | -0.40945230508 | 0.00685122334584 | 0.414679862784 | -0.0604617735392 | 0.406711210845 | -0.00803707269294 | -0.00256863360727 | 0.448980326264 | 0.0381978191186 | 0.251722883214 | 17.1911239005 | 25.6149931175 | -16.8670704441 | 4 | 4.47248840455 | 0.200472334172 | 0.116173470943 | 7.08359788579 | -1.61054397099 | 5.28087925223 | -0.0104616969115 | -0.384086232785 | 0.0404247061095 | 0.122166091682 | 0.157890457226 | 0.0693078342825 | -0.548907481933 | -0.0119880971495 | -0.115291160692 | 0.279305375172 | -0.00318037213748 | 0.0139833985102 | 0.374209136069 | -0.0255917049475 | 0.211848464779 | 14.6989089711 | 25.8663189403 | -6.85211638679 | 5 | 3.71422438383 | 4.06891611826 | 5.6645316073 | 5.43871769849 | 6.15941025186 | 9.64428450012 | 0.641362362111 | -1.78892527595 | 0.958081644038 | 0.286145546765 | -0.707633577334 | 0.481642306891 | 0.629991337787 | -1.75327975272 | 0.0308368126734 | 0.333874893545 | 0.0100175507051 | 0.0312387522087 | 0.705235937947 | -0.0810929600589 | 0.367836362135 | -0.583039276683 | 17.0828056593 | -11.4243513325 | 6 | 5.56451261768 | -4.77313670538 | -0.214392261465 | 7.4341240823 | -2.73780184959 | 6.25944388775 | 0.88585923663 | 0.212999453401 | -1.09393761847 | 0.173418812469 | -0.192023593709 | -0.291915616263 | 0.756035233769 | -0.00466009284125 | -0.685369363789 | 0.324224432984 | 0.0326982025874 | -0.0311252810646 | 0.381552784437 | -0.0355300426541 | 0.204603186417 | 14.1829012554 | 17.6144963257 | -6.63025297369 | 7 | 8.68885513593 | 4.32453035493 | 1.92609623612 | 5.9634802629 | 1.96924752214 | 8.34281604406 | 0.394889782062 | -0.480827378122 | -0.372676488942 | 0.0380289133968 | -0.168970194189 | -0.2636632533 | 1.06067129925 | 0.622706556437 | -0.282063978341 | 0.319708897485 | 0.118381718426 | -0.0354465482266 | 0.429718560656 | -0.00935923037547 | 0.302318008913 | 19.2233971829 | 14.8055447797 | -8.5880448287 | 8 | 2.91007810191 | 3.32277542291 | 2.86520588252 | 9.81444435922 | 2.99772030479 | 6.9116179375 | 0.0764439839752 | 0.0728262541137 | 0.0405370670481 | -0.344517072543 | -0.173997701794 | -0.831898763637 | -0.333128499099 | 1.20289400313 | 0.0210867962846 | 0.328380299288 | 0.038825574464 | 0.0342213196984 | 0.602179292735 | 0.0125463044497 | 0.345496907996 | 21.4781010967 | 23.7439242905 | -14.7198316294 | 9 | 4.09593490771 | -4.34814641639 | 2.10399280946 | 5.35310660728 | -0.324361497789 | 8.9196797832 | 0.16917000681 | -1.10482603704 | -1.07625742718 | -0.536145035227 | 0.260047257297 | 0.88038348495 | 2.25724766339 | -0.148850806752 | -0.350223443145 | 0.731914912259 | -0.00180218401538 | -0.0562549543637 | 0.456283393175 | 0.0696564246448 | 0.436448588554 | 9.00017567515 | 9.60725652623 | -19.7426604492 | 10 | 0.30141752966 | -0.590818762226 | 1.29387123782 | 0.813099598178 | -0.980250697878 | 4.30151259939 | -0.0788678137353 | -0.0912696292716 | -0.131265200694 | 0.0181551118186 | 0.0574435173548 | 0.0109451974774 | -0.115156019122 | -0.287050505434 | 0.0702626644062 | 0.210955435057 | 0.00695201910637 | 0.0212364360921 | 0.425437209189 | 0.011520955463 | 0.304888354903 | 17.0905925463 | 18.1893846213 | 5.03270470062 | 11 | 2.86989329968 | -2.49635464246 | 1.63371201892 | 3.55752275652 | -3.21169032948 | 3.24027723982 | -0.585662981717 | 0.140250688755 | 0.429271042031 | 0.212370994366 | 0.518926105091 | -0.709135714005 | -0.685995429017 | -0.710617866619 | 0.0794439046421 | 0.403535433942 | 0.044290406855 | 0.00270243028 | 0.437876100262 | 0.0389536745314 | 0.301778600978 | 14.4243147119 | 24.6644632046 | 16.5936188959 | 12 | 5.94112919509 | -2.89450308056 | -0.31454356981 | 9.64970416437 | 2.97327187895 | 3.5599355245 | 0.19173570883 | -0.248548982365 | -1.15805519751 | 0.846044346398 | -0.740630922233 | 0.707435990628 | 0.585745058551 | -0.61614706517 | 0.512097841105 | 0.368863259089 | -0.10799606028 | 0.0825200951545 | 0.439482510282 | 0.0516725736302 | 0.414405662649 | 14.4660307623 | 9.45613747993 | 18.1845946581 | 13 | 8.81863410389 | -4.73422772043 | 3.07204095506 | 8.28173973269 | -1.36014487138 | 6.47267184776 | -0.206892291984 | -0.220852690402 | 0.278060687606 | 0.181922883297 | 0.208198740814 | 0.182816852085 | -0.578752093988 | -0.779154759654 | 0.0219290163541 | 0.259681825892 | 0.0281816041969 | 0.0264050361983 | 0.4563603234 | -0.0279741156721 | 0.261163119831 | 14.2301752563 | 20.8172842939 | 8.13225742071 | 14 | 4.43080503989 | -3.62368458257 | 5.30445318978 | 3.47443001288 | -3.53352021925 | 7.45458660896 | 0.655075036915 | 1.1859468995 | 0.400205803825 | -0.263172574752 | -0.741894380329 | -0.440414400939 | 0.279512010672 | 0.664048341471 | 0.0458578019142 | 0.316837366822 | -0.0373177819012 | 0.0555188601217 | 0.486245396911 | -0.00465867549537 | 0.378117655229 | 21.3698545404 | 13.9080878423 | 5.7789466535 | 15 | 6.41173162834 | -6.81079838483 | 3.95379553253 | 8.25331021548 | -5.40087937205 | 7.62843991856 | 0.738715702599 | 0.624170578564 | -0.772048820677 | -1.02438997265 | -0.27053079495 | 0.143256197707 | 0.909004049002 | 0.114617414902 | -0.466454974332 | 0.368418834748 | -0.0726156934491 | 0.00118290028303 | 0.485135391804 | -0.183204101331 | 0.582740688247 | 12.0031719203 | 9.29344809599 | 2.12526121056 | 16 | 6.92646077412 | -3.80637993706 | -0.516143584061 | 9.83057470552 | 3.25862536776 | 6.34367619341 | 0.114783093 | 0.32020979385 | -0.427189179601 | 0.482947325749 | -0.385423081234 | 0.594854242226 | 0.177161866184 | -1.16640847733 | 0.246591652085 | 0.290314607006 | -0.0341360416834 | 0.0489367847465 | 0.535216851617 | 0.0146354211647 | 0.321914860497 | 7.14493146196 | 13.8955907549 | 12.3057036214 | 17 | 3.58628880102 | -2.93956377659 | 0.448690341262 | 5.34960573225 | -2.70830891257 | 4.87822673547 | 0.224419231768 | 0.206903643154 | -0.653891832875 | 0.383867187077 | -0.534952011695 | 0.539137520357 | 0.0982913316804 | 0.0251068866969 | 0.286727763312 | 0.206141386882 | -0.0392316524781 | 0.0254886309415 | 0.405678355105 | -0.0615302831765 | 0.399911253448 | 19.841058851 | 10.0273792474 | 11.64174642 | 18 | 3.03188119226 | -0.373008720484 | 1.81197566314 | 1.04249585521 | -2.06832318347 | 4.38406017415 | -0.0232703285675 | -0.185689811874 | -0.0287371963189 | -0.173304144603 | 0.114170903145 | -0.071045159281 | 0.00102487587296 | -0.449547133619 | 0.0578184077866 | 0.255717183991 | 0.0108737076645 | -0.0138513211508 | 0.45825740041 | 0.0204654025605 | 0.285766245797 | 7.51280256091 | 21.9139032556 | -15.4800255866 |
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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 7 )AA1 - 7 | 1 - 7 | 2 | 2 | chain 'A' and (resid 8 through 17 )AA8 - 17 | 8 - 17 | 3 | 3 | chain 'A' and (resid 18 through 26 )AA18 - 26 | 18 - 26 | 4 | 4 | chain 'A' and (resid 27 through 39 )AA27 - 39 | 27 - 39 | 5 | 5 | chain 'A' and (resid 40 through 45 )AA40 - 45 | 40 - 45 | 6 | 6 | chain 'A' and (resid 46 through 52 )AA46 - 52 | 46 - 52 | 7 | 7 | chain 'A' and (resid 53 through 72 )AA53 - 72 | 53 - 72 | 8 | 8 | chain 'A' and (resid 73 through 82 )AA73 - 82 | 73 - 82 | 9 | 9 | chain 'A' and (resid 83 through 91 )AA83 - 91 | 83 - 91 | 10 | 10 | chain 'A' and (resid 92 through 113 )AA92 - 113 | 92 - 113 | 11 | 11 | chain 'B' and (resid 1 through 7 )BD1 - 7 | 1 - 7 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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