Software Name Version Classification PHENIX1.20.1_4487refinement DIALSv1.0data reduction DIALSdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 1.32→25.17 Å / SU ML : 0.2319 / Cross valid method : FREE R-VALUE / σ(F) : 1.33 / Phase error : 24.0494 Stereochemistry target values : GeoStd + Monomer Library + CDL v1.2Rfactor Num. reflection % reflection Rfree 0.1923 15121 5.06 % Rwork 0.1673 283583 - obs 0.1685 149352 95.2 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 26.22 Å2 Refinement step Cycle : LAST / Resolution : 1.32→25.17 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 4942 0 12 877 5831
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.0183 5177 X-RAY DIFFRACTION f_angle_d1.507 7045 X-RAY DIFFRACTION f_chiral_restr0.1119 756 X-RAY DIFFRACTION f_plane_restr0.0171 919 X-RAY DIFFRACTION f_dihedral_angle_d7.5788 755
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 (%)1.32-1.33 0.4252 235 0.4318 4289 X-RAY DIFFRACTION 43.15 1.33-1.35 0.4091 311 0.4265 6350 X-RAY DIFFRACTION 63.97 1.35-1.37 0.4289 513 0.4096 8522 X-RAY DIFFRACTION 85.89 1.37-1.38 0.4132 509 0.389 9355 X-RAY DIFFRACTION 94.34 1.38-1.4 0.3831 581 0.3757 9464 X-RAY DIFFRACTION 96.51 1.4-1.42 0.3439 536 0.3593 9685 X-RAY DIFFRACTION 97.32 1.42-1.44 0.3757 546 0.3479 9683 X-RAY DIFFRACTION 97.54 1.44-1.46 0.3451 472 0.3213 9713 X-RAY DIFFRACTION 97.57 1.46-1.49 0.3189 533 0.301 9626 X-RAY DIFFRACTION 97.91 1.49-1.51 0.3014 577 0.2714 9676 X-RAY DIFFRACTION 98.03 1.51-1.54 0.2623 534 0.2507 9755 X-RAY DIFFRACTION 98.07 1.54-1.56 0.2672 496 0.2436 9840 X-RAY DIFFRACTION 98.3 1.56-1.59 0.2668 509 0.2352 9728 X-RAY DIFFRACTION 98.4 1.59-1.63 0.2385 548 0.2201 9757 X-RAY DIFFRACTION 98.44 1.63-1.66 0.2412 555 0.21 9772 X-RAY DIFFRACTION 98.75 1.66-1.7 0.219 589 0.1902 9767 X-RAY DIFFRACTION 98.77 1.7-1.74 0.198 495 0.1696 9826 X-RAY DIFFRACTION 98.71 1.74-1.79 0.2012 484 0.1644 9844 X-RAY DIFFRACTION 99.17 1.79-1.84 0.186 456 0.1569 9938 X-RAY DIFFRACTION 99.05 1.84-1.9 0.1887 499 0.1587 9881 X-RAY DIFFRACTION 99.15 1.9-1.97 0.1859 475 0.1572 9867 X-RAY DIFFRACTION 99.46 1.97-2.05 0.1765 511 0.1527 9908 X-RAY DIFFRACTION 99.47 2.05-2.14 0.1799 527 0.1511 9918 X-RAY DIFFRACTION 99.5 2.14-2.26 0.1798 506 0.1526 9879 X-RAY DIFFRACTION 99.75 2.26-2.4 0.1722 570 0.1406 9876 X-RAY DIFFRACTION 99.59 2.4-2.58 0.1659 567 0.1394 9886 X-RAY DIFFRACTION 99.88 2.58-2.84 0.161 474 0.1383 9963 X-RAY DIFFRACTION 99.96 2.84-3.25 0.1672 498 0.1399 9958 X-RAY DIFFRACTION 99.98 3.25-4.09 0.1716 485 0.138 9978 X-RAY DIFFRACTION 100 4.09-25.17 0.1469 530 0.1405 9879 X-RAY DIFFRACTION 99.52
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 32) 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 3.83398708671 -2.85228335609 2.94477093666 5.91822260502 -2.42380852077 5.22242522123 -0.0685981628626 -0.255584741043 0.378792716569 0.159080501828 -0.323561675906 -0.565451322324 -0.368824249508 0.444511858674 0.441841374493 0.197349833272 -0.0783227419751 -0.0159394445093 0.323031618391 0.0114684570268 0.258615778436 11.2780107812 -40.1797378451 27.7411518259 2 7.70649761919 0.443135678966 -1.48381962182 3.631249099 1.09870722926 2.72835935456 -0.0977856474674 -0.36744320072 -0.311022875395 0.217958503993 -0.0234658136381 0.00606523064563 -0.116436079126 0.233673192323 0.127260543744 0.221486480202 0.00323953132154 -0.0327872353358 0.273988299925 0.0289796955245 0.203661683253 11.2060703124 -58.2394354798 42.1836611465 3 1.62608931393 -0.425455172417 0.725393032171 2.44457375183 -0.490347555398 2.39360729456 -0.0227083009521 -0.34265222894 -0.0641143672271 0.103664898059 0.0552030908954 0.0976035668536 -0.0299447328719 -0.109054490165 -0.0426796220341 0.146564350552 -0.00413706788143 0.00459422136616 0.308580856176 0.0291191751433 0.168577495237 1.00245204169 -48.371114682 32.2618741335 4 6.66378920872 -1.69416352947 -3.86965339771 6.13649354244 1.36338159171 2.28959453361 -0.170415231203 -0.053371700696 -1.15883165313 0.0420167846793 0.0433148926276 0.22990265095 0.554973179264 -0.584095862032 0.0833127771359 0.233760923262 -0.0361776707127 -0.0196940016733 0.257499384523 0.00785654484119 0.288538919714 6.2327962367 -62.9820676127 36.9250176641 5 1.07883324504 0.409509855329 -0.66783153498 1.29995118781 -0.529775897014 2.0969234494 0.0840782685032 -0.0755127622216 0.0333584829497 0.121297960403 -0.0648708524621 -0.0154430500657 -0.1909509458 0.207434324031 -0.0136080295825 0.168658178753 -0.0105340236443 -0.00984064823935 0.240230709368 0.00184408406366 0.160958105588 4.72933393818 -42.8164276209 23.7747076908 6 6.06475652029 -2.44091590623 1.61175006134 2.77075677058 1.28823940855 2.63489308813 0.080459269703 0.568394993847 -0.243410017212 -0.278084427208 -0.289550113978 -0.411071607918 0.357192982676 0.165328440206 0.348586909434 0.171708466244 0.00671655994063 -0.000623550858151 0.271033442404 0.0218675067666 0.184428321464 13.7379320703 -58.1927763962 35.421935994 7 3.58538914773 -2.75463335089 -1.68303187286 3.72057851214 -2.45364258008 9.52317656494 -0.455626002467 -0.694736933299 -0.0552315839217 0.771938936008 -0.0549522337923 -0.439395062448 -0.720298461468 0.37346164484 0.459758302357 0.35833975299 0.0065739159719 -0.0571579612049 0.318316333763 0.0375930135443 0.300973656289 18.4930576558 -63.6651919782 47.1288215113 8 2.2766693222 -1.19454743612 -0.937498270326 2.31014542389 -0.0369071818424 1.8277798537 0.0270419381811 0.192820507161 -0.120520798628 -0.188386729055 -0.106655884181 0.240405898703 -0.0931595542376 -0.354749595814 0.0365082792564 0.140450048146 0.00342783234354 -0.0147766547758 0.156470734444 -0.0360565726657 0.153770395014 -21.2507241831 -35.6763650363 8.88630663341 9 0.826988967247 -0.452026101 -0.0158977241054 1.79819705625 -2.14147556323 8.71954304409 0.0521321098378 0.0476335933806 0.053171832131 -0.199626599537 -0.123381920508 0.274299584723 -0.45656376347 -0.571576267685 0.0732432708461 0.269745805843 0.0571077128936 -0.0131037403468 0.264663458864 -0.0415366867436 0.239754883549 -28.363538851 -29.1235725802 14.850986317 10 4.30479118036 -5.9957884039 4.07798042881 8.44802813277 -5.79897528924 4.19963649646 -0.0104606518739 0.609926038055 0.187370492341 -0.282846280694 -0.191447127113 -0.238551021321 -0.598155342981 0.303463588294 0.328164420698 0.302539835288 -0.00336691833188 -0.00631813160228 0.259320362 -0.0104195332397 0.186166435877 -16.3570264525 -30.0091524627 3.88604947368 11 1.47387394539 0.745004986859 0.168477778494 2.06570757082 -0.0646273666119 2.30207828315 -0.0860878657985 0.0268380303635 -0.166368215899 0.13274525393 0.0508315480364 -0.242209722091 -0.0472638059776 0.344744915003 0.0478109536129 0.199055593851 0.0204721421965 0.00620820529382 0.236086500087 0.0415756456473 0.186650219385 -16.1217933569 -35.5971783056 50.5173092672 12 5.10116221348 2.90892603477 4.58020035297 3.36055590261 3.27122992781 4.40490892384 -0.292741565853 0.373729008102 -0.0500529688888 -0.177622677566 0.162691666185 0.0216545799436 -0.270867277252 0.318531342006 0.119405972325 0.198189238064 -0.056121965679 0.0120002075993 0.213247765819 0.00920654687437 0.153156997301 -15.4421728984 -31.1693296755 39.5935797214 13 0.806167096974 0.105518786801 0.951636348925 0.565105419856 0.0380237840961 3.80162069296 -0.132913915343 0.142411379641 -0.114405155613 -0.0821719852302 0.104320176555 -0.0150255886227 -0.125699342088 0.150063938188 0.0686950124953 0.168414874284 -0.0347526516473 0.0141471406532 0.198817808121 -0.00737457412463 0.163494064542 -21.6366527016 -35.7159849329 33.4455863257 14 0.240993250904 0.203284055222 1.41420260786 0.139461381391 1.09529731126 7.72981000383 0.0233607906836 0.025542213334 -0.291908823923 -0.0989722982672 0.160672713532 -0.19266589567 0.0475661290431 0.903388369971 0.0519876738924 0.30290387718 -0.0841378832917 0.00512109943757 0.429534381802 0.00882220608713 0.255385503663 -9.0839526216 -30.0914538375 33.9849805028 15 3.51599331904 1.28312462514 0.704956205213 2.90431215535 1.05148638492 1.70675495075 -0.140599533414 0.128138796406 0.0157235638929 -0.0798523599903 0.144093994632 -0.0352206446204 -0.356916020886 0.0987265963873 -0.0219212548202 0.21287714313 -0.0323267286994 -0.0063752105456 0.187007012758 0.0195277954769 0.140682025037 -17.7688242965 -27.1971614748 45.0958517992 16 5.46849088025 1.06567846494 0.9913973629 6.51937868351 0.841692347973 7.80041124607 0.384072999065 0.0163398615273 0.235617353823 -0.0115622504626 -0.304903206001 0.617771370277 -0.443370572202 -0.347839304585 0.103699344614 0.26001869157 0.0129809356796 0.050691238357 0.269260279257 0.0338256757973 0.285217835001 -28.9855258938 -28.7974481765 44.2869389907 17 6.58597473812 0.248173968093 1.48032540581 3.51086308609 -0.738291699878 0.558179067379 -0.0280036009541 0.00385867578927 -0.310568903152 0.10822643909 -0.0585212920676 -0.121587604187 0.192490763722 -0.0831034319638 0.17929288749 0.205040655864 -0.0176626182831 -0.024899240062 0.181956014909 0.0292542105224 0.12586179109 -47.2443706781 -57.3775760255 42.4571800301 18 1.9194481403 1.12013139484 -0.774789910699 2.65026819979 -0.144972293879 3.31661393425 0.0349650791276 -0.175316103995 -0.0676950552833 0.181961003611 -0.0544280127949 -0.18225918546 -0.0352212116184 0.318640053075 0.00958376743986 0.141205565435 -0.0075835418791 -0.00808634965418 0.215893989 -0.0121101679199 0.145394488295 -39.9192180522 -48.5620515972 38.5322598406 19 5.23517901522 -2.52971207909 -0.139611682577 5.76457137987 -1.14612970343 3.69086053477 0.113628725717 -0.0800156690422 0.174885388312 0.491702044906 -0.154777337498 -0.330295806553 -0.24889282485 0.176061444694 0.0418675502756 0.240430433803 -0.062413683542 -0.0188729349391 0.232343969053 -0.030159907549 0.171517995893 -43.0461499992 -44.9395913652 44.0320765981 20 1.95757177254 1.35845222982 -0.506001934624 1.21243369552 -0.142204146256 0.474105712845 0.0507313864448 -0.0880829488025 -0.0569742557767 0.0224338911847 -0.0511972516008 -0.0694549146239 -0.0367420030715 0.0387995608795 -0.00244619999217 0.161919901534 -0.00756766020425 -0.0139431561559 0.19536041389 0.00378042561655 0.156668033757 -41.3617267 -48.6766820086 37.3763365311 21 1.8014785271 1.20351000698 0.962824228736 4.37308612734 3.32309014605 5.55729608845 -0.0697338157092 -0.104835227813 0.245338449445 0.0518908717181 -0.109594059469 0.435032039862 -0.118852904887 -0.565743340828 0.0481393834903 0.157513380572 0.0578901396314 -0.00761609256122 0.24899356009 -0.00486618233483 0.195298751095 -49.9062548902 -39.7283680101 22.4268768049 22 4.01697291176 -0.31170743119 -0.685868563396 3.19112780134 1.00388813515 0.689189423551 0.00459256287567 0.447312871377 -0.407204659444 -0.265185358649 -0.0633946228152 0.0028265294649 -0.267534434828 -0.168430789339 0.046753200669 0.230439043598 0.0115616408298 -0.0568389880155 0.297590590025 -0.0755460023463 0.267204167548 -49.6394104317 -55.8742708611 6.12602868002 23 2.02479063523 0.353589308871 0.527301327394 1.5359328668 0.769047717353 2.02863712376 0.0399078101415 0.0789384648459 -0.111550724943 -0.0770310967764 -0.018159469627 -0.0283185749246 -0.0706135839252 -0.00251371201256 -0.0246871184789 0.136415929637 0.0105686702648 -0.00226523077318 0.189615927447 -0.0101753323345 0.153684329505 -40.9960374601 -46.9940827196 18.5625367169 24 2.60627602499 2.06296542431 2.69200392221 2.73289452993 1.81197108766 4.16104947054 0.113505592795 -3.79078603631E-5 -0.227394850284 -0.201720627173 -0.0209149116752 -0.177410692652 0.238504138035 -0.145828117526 -0.162403728164 0.183030876966 0.000123368745344 0.00342146135554 0.207435032095 -0.0495321806401 0.215863640473 -55.4901625964 -59.8872248032 5.99909435005 25 6.73886935433 -0.0142493849012 0.214689746206 2.09007786248 0.908776088318 0.643899551091 -0.0676674318932 0.0113397017123 -0.380072350552 -0.0169151349851 -0.023183873054 0.149562277292 0.128012400022 0.0492951977762 0.134956700202 0.153024911372 0.0235484248196 -0.0278428914652 0.131429332882 -0.0158956870787 0.148505575843 8.46574105967 -56.7161959408 6.32327845193 26 2.95946468941 0.207427105021 -0.890734821005 1.19861417771 -0.104979881986 0.63029556708 0.0159333722735 0.002773326881 -0.39540398504 -0.0702017038487 -0.111961828745 0.066479854782 0.12532782225 -0.0467288839409 0.0916420087418 0.19051854293 0.00951576754835 -0.0246609899816 0.192390069602 -0.0186396003123 0.192843406918 -4.20005681829 -53.8395406072 7.05855754676 27 1.33422446274 -0.543816854159 -0.334328343932 1.15958936643 -0.110238040567 1.95385633606 0.000288165267249 -0.0452180855636 0.00215871765426 0.0126310143172 -0.0245389076717 -0.0448212715321 0.0131187690787 0.188989523099 0.0107015383665 0.146037293237 -0.00531657932913 -0.00511289748557 0.168857715166 -0.00230818142894 0.148046300645 4.37816848721 -45.9827323451 13.0882847374 28 6.05735281881 -0.344396688173 -2.40529861581 3.35667117446 1.72961107583 6.13831380313 0.37409540359 -0.145297837391 0.460197898574 -0.126363421308 -0.231513440725 -0.183917325944 -0.614400930608 0.135551534301 -0.0451143269351 0.276755266449 -0.0218658671788 0.0293882354891 0.21884075019 0.0155648188355 0.228334932728 10.593753293 -38.4333413685 9.85118258639 29 5.40291036298 1.89631176139 -0.820511288855 1.94058944568 -0.455109774196 1.15786295869 -0.107283415952 0.296032124423 -0.187569732951 -0.180196695711 0.0563342125137 0.0884670270308 0.00536693291632 -0.169887104413 0.0514869955399 0.188923379498 0.012848054602 -0.0194271840056 0.196261042014 -0.0218829601291 0.197911051449 0.393615673373 -49.9271802753 3.04119847064 30 2.92613822783 -3.88717963001 2.82885010464 5.22781131302 -3.84841615642 2.8934363924 -0.202795460685 -0.0904118539101 0.334261322044 0.174598785922 0.107197032213 -0.31221964304 -0.412296749489 0.194329430893 0.25506405229 0.183560140146 -0.0113212797377 -0.00933646942286 0.242711833957 -0.00181889470746 0.198921281052 18.1107302682 -46.714229536 6.26560117016 31 2.36137734989 -0.84795965065 -0.01374164866 0.588162589155 -0.075360831445 0.59628136036 0.0472073977165 -0.204538749458 -0.0678440493192 -0.0114947423834 -0.00210377293536 0.0595061739268 -0.0181755022075 0.0047738009759 -0.0389225399075 0.168194093397 0.00190877089194 0.00436686665019 0.168786929856 -0.00746301428902 0.17390205158 -5.91752941163 -45.4179573239 16.2123446754 32 9.55938317203 -0.128258534925 -2.68850936258 0.211881425707 0.1426105194 2.45171076468 -0.104864800545 0.0939067496137 -0.0100702366659 -0.00569483574905 0.0864170035415 0.0239482669985 0.0788890993196 0.101807092241 0.0111728513679 0.163193794127 0.0385863953309 -0.0105794478405 0.146560236039 0.0117226979321 0.191105802177 11.2696598006 -54.7186828455 11.1212432877
Refinement TLS group Refine-ID : X-RAY DIFFRACTION
Show large table (7 x 32) Hide large table ID Refine TLS-ID Selection details Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 1 chain 'C' and (resid 145 through 154 )CA145 - 154 1 - 10 2 2 chain 'C' and (resid 155 through 163 )CA155 - 163 11 - 19 3 3 chain 'C' and (resid 164 through 224 )CA164 - 224 20 - 80 4 4 chain 'C' and (resid 225 through 232 )CA225 - 232 81 - 88 5 5 chain 'C' and (resid 233 through 252 )CA233 - 252 89 - 108 6 6 chain 'C' and (resid 253 through 258 )CA253 - 258 109 - 114 7 7 chain 'C' and (resid 259 through 263 )CA259 - 263 115 - 119 8 8 chain 'X' and (resid 1 through 45 )XC1 - 45 1 - 45 9 9 chain 'X' and (resid 46 through 60 )XC46 - 60 46 - 60 10 10 chain 'X' and (resid 61 through 72 )XC61 - 72 61 - 72 11 11 chain 'Z' and (resid 1 through 21 )ZD1 - 21 1 - 21 12 12 chain '