Software Name Version Classification PHENIX1.19.2_4158refinement XDSdata reduction XDSdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 2PGSResolution : 2.32→37.86 Å / SU ML : 0.4081 / Cross valid method : FREE R-VALUE / σ(F) : 1.33 / Phase error : 31.1055 Stereochemistry target values : GeoStd + Monomer Library + CDL v1.2Rfactor Num. reflection % reflection Rfree 0.2517 11887 4.58 % Rwork 0.2184 247401 - obs 0.22 259288 98.59 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 79.38 Å2 Refinement step Cycle : LAST / Resolution : 2.32→37.86 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 18255 0 6 132 18393
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.0092 18654 X-RAY DIFFRACTION f_angle_d1.149 25280 X-RAY DIFFRACTION f_chiral_restr0.1524 2784 X-RAY DIFFRACTION f_plane_restr0.0084 3303 X-RAY DIFFRACTION f_dihedral_angle_d25.0187 6752
LS refinement shell Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.32-2.35 0.388 362 0.3992 7515 X-RAY DIFFRACTION 89.41 2.35-2.37 0.3701 394 0.3903 8212 X-RAY DIFFRACTION 98.56 2.37-2.4 0.3935 394 0.3772 8286 X-RAY DIFFRACTION 98.83 2.4-2.43 0.3874 400 0.367 8279 X-RAY DIFFRACTION 99.2 2.43-2.47 0.363 399 0.3608 8314 X-RAY DIFFRACTION 99.14 2.47-2.5 0.377 395 0.3436 8326 X-RAY DIFFRACTION 98.53 2.5-2.54 0.3536 391 0.3352 8107 X-RAY DIFFRACTION 98.21 2.54-2.57 0.3235 399 0.3154 8215 X-RAY DIFFRACTION 97.98 2.57-2.61 0.333 397 0.3137 8315 X-RAY DIFFRACTION 99.65 2.61-2.66 0.3498 398 0.3087 8347 X-RAY DIFFRACTION 99.94 2.66-2.7 0.3316 404 0.3033 8395 X-RAY DIFFRACTION 99.98 2.7-2.75 0.2943 399 0.2906 8329 X-RAY DIFFRACTION 99.93 2.75-2.8 0.3197 409 0.2751 8378 X-RAY DIFFRACTION 99.84 2.8-2.86 0.3283 401 0.2656 8311 X-RAY DIFFRACTION 99.9 2.86-2.92 0.2857 406 0.2591 8379 X-RAY DIFFRACTION 99.8 2.92-2.99 0.3107 405 0.2552 8365 X-RAY DIFFRACTION 99.83 2.99-3.07 0.3165 403 0.2707 8337 X-RAY DIFFRACTION 99.81 3.07-3.15 0.3176 399 0.2723 8299 X-RAY DIFFRACTION 99.44 3.15-3.24 0.3317 400 0.2604 8308 X-RAY DIFFRACTION 99.37 3.24-3.35 0.2636 399 0.2427 8282 X-RAY DIFFRACTION 99.25 3.35-3.47 0.2947 389 0.2373 8303 X-RAY DIFFRACTION 99.03 3.47-3.61 0.2514 402 0.2302 8227 X-RAY DIFFRACTION 98.24 3.61-3.77 0.2425 386 0.1973 8041 X-RAY DIFFRACTION 95.99 3.77-3.97 0.2508 398 0.2017 8251 X-RAY DIFFRACTION 99.11 3.97-4.22 0.238 395 0.181 8306 X-RAY DIFFRACTION 99.04 4.22-4.54 0.1949 392 0.1667 8263 X-RAY DIFFRACTION 98.88 4.54-5 0.1941 393 0.1732 8296 X-RAY DIFFRACTION 98.74 5-5.72 0.2626 390 0.1987 8223 X-RAY DIFFRACTION 98.58 5.72-7.19 0.2224 393 0.2053 8058 X-RAY DIFFRACTION 96.38 7.2-37.86 0.1763 395 0.1665 8134 X-RAY DIFFRACTION 97.15
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 24) Hide large table 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 2.39568724647 0.245916404819 0.790712651723 2.84252458563 -0.154627406937 2.62483804433 -0.0569641146616 -0.137093124425 0.230754217533 0.428009852757 0.0336134149348 -0.0772571135253 -0.213545055743 0.129832420222 0.00589859163122 0.465334768798 -0.0146830496809 -0.0548073226944 0.398797725471 -0.019150780288 0.386601005601 83.7417935776 112.648866685 70.9511794616 2 4.88033056766 -6.10144638279 -0.0382666629858 9.99261262615 1.12331422835 6.50070262521 -0.00925841423652 0.119323543994 -0.146677444241 0.471652462721 0.271146258607 -2.58159624318 0.0860012412127 0.599198491363 -0.349077784039 0.658480420871 -0.0468647441465 -0.135051313282 0.932560896223 -0.0353693866412 0.976150652609 94.8720812182 107.419287106 57.7590593119 3 0.618254711602 -1.27722726017 1.45402106449 2.87373576455 -4.40678003756 8.52430217912 -0.0554118790771 0.219443337106 0.307661873976 -0.36068640141 0.0507407846487 -0.117317561975 0.241579370966 0.505894257808 -0.000611405680624 0.639527825008 -0.0728142512831 -0.0850410488866 0.733754270395 -0.0453374686104 0.584547418646 93.7611082035 112.327319012 70.2941597073 4 1.42821237519 0.063656852634 0.711021984428 1.92740184639 0.458032616594 2.61427442765 0.113623347649 -0.122046611871 -0.0850172301112 0.409362290559 -0.0645606660942 -0.288053922315 0.323677435164 0.292985556606 -0.0918596026173 0.512202520712 0.0083462123505 -0.0263682241943 0.505317145409 -0.00779509267595 0.503871126758 90.7122263734 97.5855364378 71.8099243959 5 2.39397548861 -0.61883019429 0.181268543425 3.67971994815 0.103720337646 2.05574688848 -0.00202248124592 -0.209658396973 -0.0339329183604 0.274552984493 0.10295224255 0.113872248662 -0.0556108825159 0.12618728737 -0.0814219421971 0.667580918785 0.0378182100208 0.0960721643774 0.506742652131 -0.0403629784086 0.468292986677 69.0717337569 102.581396754 91.5468353893 6 0.756583080305 0.119846681457 1.10901589343 1.74853182579 -1.93723770494 4.63670976383 0.0326038899735 -0.272682300441 0.119322437211 0.601482690583 0.189565872627 0.515796606021 -0.0816199532992 -0.0909955554436 -0.278382494537 0.724453721017 0.0832415864211 0.227697197667 0.623027677295 0.0320510654062 0.761931819777 59.1835556665 105.013370006 94.5619152754 7 2.59629639027 -0.75978464917 0.315931632717 3.35149243191 -0.0126381479239 1.85577926062 0.191531596533 0.179830403171 0.0355502087429 -0.370221764629 -0.145856467591 0.212696402612 0.0946812051774 -0.0553254256444 -0.0458878290259 0.514574130515 -0.00743368027939 0.0235452527278 0.469051436158 -0.0253623542761 0.447397499302 51.9340675539 77.6235955075 27.0321243607 8 9.76094236291 2.10692607646 8.98213104619 6.39390113478 1.03231173123 8.84413960085 -0.653370743054 1.32217531243 2.05684939969 -1.092939622 -0.097719854481 0.544858198395 -0.735796635258 1.29915724048 0.655849084304 0.724063969188 0.0436552707885 0.173901664281 0.889651429203 0.163734582132 0.959570538113 70.59948978 87.6875714002 26.6160173494 9 3.02772046123 -1.67436921628 -1.22984090902 4.41624592803 3.18885775531 4.40156124316 -0.00984843558696 0.508438970523 0.10906802725 -0.792664098554 0.0106258036323 -0.266109447343 0.172611964544 0.515900077829 -0.0477770514785 0.682152531167 0.0410754035221 0.0269980937803 0.56523945368 0.074317999167 0.576130905756 54.0927207345 86.2974361825 22.3206852346 10 2.44758158855 -1.25203878183 0.347123132351 3.24938937106 -0.186385431839 0.616031999713 -0.0906386112711 0.0112560980928 0.270194468868 -0.0297170372139 0.113050358875 -0.155529185983 -0.0539824052109 -0.00802961713608 -0.0134580716884 0.475844453806 -0.0488662816923 -0.000329218263947 0.49023339998 0.016114611199 0.475800630272 57.1611923644 89.1056847262 36.5275675382 11 1.26799691948 0.18289629991 0.804804107777 2.84848351627 0.549705486736 2.78633892995 -0.0423991483982 -0.0488400059354 0.0720396987088 -0.0603437731462 -0.00647902313353 0.529781010369 0.148810741418 -0.223937438288 0.0455158343604 0.477955865691 -0.0286876014069 0.0845696419156 0.526571151175 0.0267271105146 0.679355717536 33.0710168727 74.6059459864 46.7175563425 12 9.1898218827 1.47153935313 5.36675682095 7.0963661647 -0.341720669815 3.3993611127 0.703846432734 -1.74350535968 -0.28823874346 0.33686564586 -0.187333329039 0.771857884976 1.52421560445 0.150068750871 -0.578397156053 0.909445757851 -0.0174623827684 0.158248135234 0.929728513439 0.118914752306 0.852982559466 32.085595298 64.5417240108 64.5999811504 13 1.84284079621 -0.438245702335 0.0337204752708 4.82553779896 -0.602002212417 1.76463084668 -0.184773946483 -0.0490094523737 -0.0366780658939 -0.351721835192 0.0428021113441 -0.838626838167 0.201995464113 0.307709804475 0.162819359443 0.446562443973 -0.0180937645487 0.123048168946 0.55958509708 -0.00387746991036 0.837488321698 99.7264966755 49.2512246086 61.8962161924 14 1.56555604708 -1.49190283803 -1.17007202704 5.96584071826 -2.87267432136 4.38574001187 -0.0789724531264 -0.660782003618 -0.328962582988 -0.895542189891 -0.793346063887 -1.10797016587 0.855410962049 0.533037609678 0.770003150781 0.562156034666 -0.138007015884 0.325509298741 0.661694560597 -0.0553371718408 1.21808556872 102.625038491 58.2468434091 49.1591915589 15 4.75628366059 3.83488975427 1.75414078933 4.35690242722 0.0394362255342 1.88874124785 -0.181676932302 0.0802914156072 0.295559299079 -0.768781397155 0.0204189011302 -0.871036011033 0.172837624464 0.40308624405 0.138898340794 0.820386636747 -0.0558993586239 0.300668741968 0.650542285413 0.00117919293571 0.882710141978 100.911742884 46.491164401 53.2060178691 16 2.51930578408 -0.492768818042 0.220121780539 3.85977643808 -0.366771021143 2.41644357054 -0.0237549430501 -0.05754569722 -0.227537412605 0.1651385788 0.0791137642186 -0.0898800673006 0.162602847674 0.140996334663 -0.0332009562211 0.424181769041 -0.0178421607815 -0.0132229014299 0.485902625082 0.00225372666116 0.546454351457 79.1814551993 39.411831767 76.8949102672 17 9.37132451637 -7.38366661531 -2.61426378524 5.87814830107 1.65878666589 6.16216876976 -0.834716934786 -0.824539561508 -0.547193605245 0.947251373088 0.479664422226 0.98313342832 0.368477595489 -0.252207616123 0.370801869677 0.690094657783 0.0151686105042 0.0776740267799 0.751066683391 0.0513887138844 0.868821690025 63.8956748894 49.420513724 91.5181595738 18 4.76046015646 1.07583308443 0.596820819316 2.61438128499 1.48318268419 0.605362694689 -0.311884143813 -0.298439597639 0.117591708146 0.539021779165 0.350959308504 0.413135921177 0.264486859506 -0.0209515297954 -0.0530421586831 0.797175253725 0.044690486896 -0.056760951148 0.809812311668 0.0616530176832 0.696112221548 78.9844093532 39.3805835477 87.5175276065 19 9.41458904391 6.10939203965 3.96099416249 5.13658044526 4.85205083877 6.02817924952 0.508676094918 0.124940392424 1.14941356223 0.953004205773 -0.53565061097 1.97643249494 0.350052064816 -0.430838856542 0.263834582263 0.91028687816 0.0338587856035 0.21437904619 0.709080726616 0.153287350974 1.19672898548 51.1045890905 88.4800758989 92.8696750005 20 0.95873956964 -0.23180025368 0.544645582939 1.89923236745 -0.739047704918 1.40690636273 0.0381783311744 -0.179576394364 -0.0524696686212 0.133346569548 0.17431242145 0.57839277887 -0.00143477119818 -0.207152526873 -0.22285320269 0.475643123257 0.00752665542222 0.100203124787 0.425054219888 0.0171041912994 0.581596695083 58.6091727189 99.5745222307 80.9405592528 21 2.58143374994 -4.41847772816 -2.2881634508 7.95781641464 3.68038077583 3.46347805551 0.117228763725 -0.630793123158 0.40240235252 0.37965850071 0.203067929291 -0.0822823499774 0.282457276615 0.104816063558 -0.322029849779 0.655154131545 -0.10315225183 0.0712319075859 0.575428317799 -0.0341312401417 0.836138972071 29.0448955723 65.2299293809 49.8625851091 22 1.26350524396 0.846826558117 0.894118781621 4.4723314228 1.57508479359 2.14033752751 0.0204370346213 0.135599567248 -0.199970050286 0.215166663108 0.227151109667 -0.110540132766 0.187519122454 0.117089077603 -0.278574362916 0.374386435823 -0.061244220105 0.0708468626948 0.413074196365 0.0339844490959 0.484941773763 43.3702859843 62.6885806462 51.9736584787 23 1.16665920172 0.464516557031 0.0526634218772 3.54164344858 -0.116797411251 1.24028679876 -0.261751006359 0.230624200964 -0.100821814666 -0.702167017536 0.169563922507 -0.252960379353 0.221363410424 0.134181554331 0.0751001513949 0.662268350236 -0.039697000608 0.075302671003 0.491519355123 -0.0101757186489 0.509591495495 87.8394515468 52.3050162724 51.3225179412 24 2.56079306291 -0.81457691428 0.969180733632 2.51982338512 -0.124760790238 1.66233907707 -0.215418303336 -0.385600699288 0.310056406917 0.488088897492 0.0840085427793 -0.218652365281 -0.0611512393815 0.0760383334509 0.153863416555 0.548384231045 0.0299995918224 0.0152803728796 0.539688479607 -0.0486575785894 0.544662133547 80.2001953541 54.0420831994 84.0629298165
Refinement TLS group Refine-ID : X-RAY DIFFRACTION
Show large table (7 x 24) Hide large table ID Refine TLS-ID Selection details Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 1 chain 'B' and (resid 5 through 167)BA5 - 167 1 - 151 2 2 chain 'B' and (resid 168 through 198)BA168 - 198 152 - 161 3 3 chain 'B' and (resid 199 through 264)BA199 - 264 162 - 213 4 4 chain 'B' and (resid 265 through 436)BA265 - 436 214 - 385 5 5 chain 'A' and (resid 6 through 167)AB6 - 167 1 - 150 6 6 chain 'A' and (resid 199 through 264)AB199 - 264 173 - 229 7 7 chain 'D' and (resid 5 through 167)DC5 - 167 1 - 150 8 8 chain 'D' and (resid 168 through 198)DC168 - 198 151 - 167 9 9 chain 'D' and (resid 199 through 264)DC199 - 264 168 - 221 10 10 chain 'D' and (resid 265 through 435)DC265 - 435 222 - 392 11 11 chain 'C' and (resid 6 through 167)CD6 - 167 1 - 147 12 12 chain '