Software Name Version Classification PHENIX1.11.1_2575refinement XDSdata reduction XDSdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.14353600683→39.7613289734 Å / SU ML : 0.333261603839 / Cross valid method : FREE R-VALUE / σ(F) : 1.33786595283 / Phase error : 25.8905696562 Stereochemistry target values : GeoStd + Monomer Library + CDL v1.2Rfactor Num. reflection % reflection Rfree 0.245384553422 1424 5.00650423654 % Rwork 0.216028462864 27019 - obs 0.217533490853 28443 96.4398331808 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 59.5208165254 Å2 Refinement step Cycle : LAST / Resolution : 2.14353600683→39.7613289734 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 3625 0 22 181 3828
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.00334216402996 3756 X-RAY DIFFRACTION f_angle_d0.539864812529 5089 X-RAY DIFFRACTION f_chiral_restr0.0447988882359 580 X-RAY DIFFRACTION f_plane_restr0.00442105461867 656 X-RAY DIFFRACTION f_dihedral_angle_d11.3334829017 2242
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.14354-2.2201 0.383973749353 140 0.336494865482 2646 X-RAY DIFFRACTION 96.035849707 2.2201-2.309 0.331768622531 143 0.304264546519 2704 X-RAY DIFFRACTION 98.2401656315 2.309-2.4141 0.31071585634 141 0.280493431779 2683 X-RAY DIFFRACTION 97.8516978517 2.4141-2.5414 0.279335299561 142 0.263843913788 2700 X-RAY DIFFRACTION 99.058905542 2.5414-2.7005 0.315846033609 145 0.239869010279 2760 X-RAY DIFFRACTION 99.3162393162 2.7005-2.909 0.254734817998 144 0.227452804977 2729 X-RAY DIFFRACTION 98.6607142857 2.909-3.2016 0.229580979734 143 0.207960026273 2716 X-RAY DIFFRACTION 97.3773841962 3.2016-3.6646 0.250397549125 140 0.191607245644 2666 X-RAY DIFFRACTION 94.861392833 3.6646-4.6159 0.194625603102 143 0.169829234642 2720 X-RAY DIFFRACTION 94.6759259259 4.6159-39.7613 0.242394896065 143 0.229246102077 2695 X-RAY DIFFRACTION 89.2452830189
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 29) 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 3.10567718148 1.37915369311 3.91566280693 0.629707658939 1.52098943823 4.93934211266 -0.359179334137 -0.285509127352 -0.207240989068 0.507322985119 -0.257688069126 1.52319232565 0.902934913624 -1.20565853119 0.0570686880869 0.530761919776 -0.224414676105 0.177978271872 0.643989501622 -0.0751827841412 0.791001230353 7.52296352109 0.462686277161 20.5281605417 2 6.39280281083 -0.20792594236 -0.410394709034 6.15412155234 -0.950197777491 8.45460500245 0.090213836478 0.0980515985089 -0.371644459145 1.15361452537 -0.436508531116 0.568218395457 -0.655236083272 -0.463990184417 0.278193658402 0.58152971936 -0.051502936104 0.138744561291 0.443709894071 -0.121042058303 0.545096525577 10.876145183 3.57717987428 11.9091535239 3 3.53746323747 0.683491200841 2.93866629427 3.68522378687 2.27570857618 3.09882822722 -0.773749854487 0.455099889172 -0.886625367229 1.44557657365 -0.080892203723 0.750669707463 0.0929903869608 0.954976883138 0.517689165709 1.09174784567 -0.171536854646 0.197673927634 0.875166841026 0.0540086366014 0.914604693942 13.8905844419 17.6823397631 7.01974947702 4 2.83056945344 -1.96465551226 0.973678803202 2.03568119256 0.693501317247 2.34331789411 0.120688246745 0.0750889597804 -0.663965683484 -0.471058844414 -0.38504210169 -0.120357403138 -0.714124120835 0.489398638743 0.206189113978 0.513274035109 -0.0721305447994 0.086156098377 0.424821319809 -0.0209431423972 0.401754692054 12.7720170459 7.36860808694 16.1226651491 5 1.70671256504 -0.789083147079 -0.637875498192 2.77271981594 1.24958909904 2.9444907575 0.0481661595989 0.126676002185 -0.159862241792 -0.206536209096 0.0501790244075 -0.0564497406036 -0.0951726820851 0.00576585103071 0.00953745647325 0.441418857886 -0.0985892581558 0.00196652752277 0.327595892684 -0.00815461734996 0.286831416523 15.7397976441 8.98769380574 17.8293689904 6 0.320952990365 -0.204893545647 0.615483338127 0.347158682348 -0.327947649701 1.47291120306 0.102851848259 -0.202165680664 -0.125438443877 -0.90135100177 0.264188806571 1.04014148439 0.324892062314 0.271068750279 -0.149552498773 0.646278287032 -0.116764167721 -0.0781105023444 0.448410349831 0.0746252512587 0.636851647614 26.0499379864 1.10786301864 14.2232123384 7 1.50031294556 -0.268761195376 -1.86611399752 0.942484311624 1.98860880928 1.41846587236 -0.272735972847 0.627740665129 0.381927835323 -0.299543235471 0.388257352672 -0.266626845056 0.101512327352 -0.136986369451 -0.0994566104716 0.473943652623 -0.126039659745 0.0693420141298 0.460703256379 0.0125471694749 0.348891408333 15.9098063318 8.79521740267 12.9404193251 8 3.22389600524 -1.59948101529 -0.288127955763 4.66630888311 -0.310335126414 3.08284447153 -0.0700220547145 0.0601126396048 0.0867220838545 -0.524227511987 -0.422139713033 -0.192361474327 0.952715557379 -0.701218033309 0.533811370108 0.617826285975 -0.210319669626 0.0520956990793 0.446313663457 -0.0315809342266 0.576926296695 13.4227554421 -1.38211108507 14.5017998359 9 3.19921533294 -0.479188920197 1.17337041432 2.60279870541 2.00147715698 2.11643987117 0.194151182717 -0.608515494346 0.0409506131505 0.586035574369 -0.20890002193 -1.47287817181 0.251588536412 0.2457861996 -0.0563909201633 0.455273584653 -0.126489411539 0.0125522814058 0.500331878436 0.0518145329866 0.422257700725 22.5895850865 6.98146931732 25.5505696079 10 9.74824552621 -2.24251741201 -3.48219917936 2.8663815089 2.43871428705 2.35482496256 -0.544048090591 -1.34417470327 0.619625548543 1.39975285289 -0.760067496393 -0.968635794095 -0.267026862184 0.984014840793 -0.0746016271167 0.855613989508 -0.17909234632 -0.0181469580811 0.711187087952 0.0161843675073 0.564672468725 20.7939244766 18.3734997747 30.4675534175 11 5.76084466436 -1.75337189001 2.46462156466 2.5560889777 -0.0754688054128 6.18626196222 -0.314424617166 -0.010559729384 0.529938374049 0.221142660212 0.0995598830831 0.129437069496 -1.37159615405 0.514917849097 0.134866962042 0.650424260461 -0.069959156887 0.0358068302667 0.464538056067 0.029755742151 0.47451146795 15.3585502708 31.2730907495 22.6257933827 12 6.74679408681 1.78457366036 -1.09726087751 6.90915659972 -1.90615894456 0.56844888373 0.28991699674 2.15395308124 0.311944889381 -1.05855158218 -0.274336301755 0.451242721788 1.3130552533 -2.81227078562 -0.319979356087 1.22952825977 -0.182338302789 0.00812726815314 1.16782103973 0.00125091794545 0.897092940512 3.54074182209 23.03966272 12.9827314574 13 3.97863448026 -0.0665466817592 -1.60110177586 1.66146272675 1.40462899794 1.02781860059 0.113617178767 0.0978696587045 0.251485604386 -0.15378140074 -0.0177102586355 -0.0389238383689 -0.326044199472 -0.031390294449 0.0490442197234 0.40880364344 -0.0489851548463 0.0320651696511 0.446496862855 0.0639650163897 0.366453798351 11.7283605847 23.8212302077 23.4741757947 14 3.58946799431 0.659762483333 2.37252139928 0.997884486825 1.43712827696 4.07047448693 -0.804851120427 -0.316540002833 0.824512811632 0.746574503857 -0.00937047898911 0.584651076206 -0.606133360993 0.127608108147 0.434172090172 0.679702684015 0.031623438005 -0.0186131395404 0.463900540731 -0.0237494238052 0.687385376072 1.98115864298 31.0954005385 31.5417623615 15 4.83237770895 0.703044377016 -2.1325150733 0.97791483603 1.01387776854 2.94422131622 -0.258678462296 0.699711400487 -0.571825860706 -0.568883258245 -0.165713947251 0.0695504221719 0.0193819324859 -0.501581361906 0.425574974836 0.56126477534 -0.0788451659667 0.0220743384925 0.373355714109 -0.0206924612224 0.384155941281 9.62026618903 22.6380750305 19.370985653 16 2.38627813878 -0.349286157575 1.10095712612 3.07234997542 -0.69315104813 0.133336683759 0.197787207406 -0.348608554254 0.486870860158 0.486253640525 -0.328879334843 -0.225890895257 -0.245230984698 0.0862642932987 0.127309266087 0.435525514169 -0.0287833052413 0.0809280104686 0.415491518026 0.0263838950218 0.435781265865 12.2261025357 25.8117622622 29.9808861699 17 0.110847004643 0.298067774235 -0.529288239001 2.12684715692 -1.30360020663 1.68714046319 -0.144929816808 -0.496495830051 -1.17512855358 0.84335886969 -0.746653669811 0.156375812532 0.45501907056 0.932995517219 0.71175696028 0.460357238332 -0.073234861957 0.139122065477 0.671855806395 0.0397574007177 0.579457115443 14.4614190384 7.51819845291 32.1732880874 18 1.87564441942 1.67875383042 0.240862916694 3.29105387637 2.26662775243 2.42732432192 -0.123651356924 0.469809379064 0.153931516107 -0.571731622143 0.371244105841 -0.496720919201 -0.481474700518 0.346916404747 -0.135390336921 0.467357699857 -0.085602424563 0.0600883270586 0.479691539249 -0.0104573842403 0.540019260112 51.0567352043 31.8058711238 11.9701450698 19 3.72380332863 0.486698090491 -1.47940591112 3.7355542195 0.479322731902 2.04011190707 -0.0817091467476 -0.253150652533 -0.0889502394365 0.534626208606 -0.0157358087801 0.0748180103347 0.431248186809 -0.155309771027 -0.0338390506318 0.678136830772 -0.100574597371 0.0794457634358 0.497417235046 0.0191804341602 0.545480625945 41.5037606713 24.3324055033 13.0050928597 20 4.29050703554 -0.358802195048 -3.44914591437 1.52228873542 -0.258217925063 2.90144962075 0.268741818694 0.783292681854 1.07502412879 0.197410553209 -0.412334819254 0.996215717377 0.766515967703 -1.65796833196 0.564921891983 0.561295065105 -0.038327277771 0.0630346443318 0.683472214222 -0.00537668737313 0.705377118573 32.6992907457 29.4580249837 6.86312031415 21 3.66927003783 2.7401744401 -0.00407571800196 7.84269401029 2.98082618478 6.21770844448 -0.265854430265 0.288144677906 0.417669947218 0.0250845578252 0.13602458056 0.151033001958 0.290132086215 -0.526163029084 0.254453411482 0.455866117915 -0.0822746139735 0.0588214375132 0.360294154024 -0.0123225569066 0.40323710558 42.0372462272 32.7492039523 7.71993411283 22 2.16974479546 2.50520295633 0.215973269093 1.32445020223 -0.346618348307 0.721486894921 0.276848630452 0.0573293877229 0.0862985699341 0.326804646732 -0.20833107357 0.175682397859 0.00935280832294 -0.258807871232 0.0630912331742 0.530045285024 -0.0970264150744 0.108685737174 0.536101749085 -0.0384552793881 0.461355259893 38.4044281059 26.2415130118 13.4883337421 23 1.81270498133 1.15737967587 0.673496199934 4.91448063023 0.909999857031 2.29970951363 0.148249728868 -0.244967338132 -0.624390889031 0.660945297359 -0.00802699538667 -0.49076112263 0.345109010059 0.1217879317 0.164690641117 0.559183581926 -0.0943890409083 0.0579493380825 0.525969710948 -0.0102347945139 0.502531995216 43.9890446645 22.2881056497 16.359990204 24 0.343430215533 0.884838913853 0.682716728866 1.0974536043 0.361793346457 1.19573226707 -0.144725682208 1.21920476584 0.448130530821 0.309235676823 -0.126216561569 1.95874030164 -0.206726711586 -1.11045541892 0.0399037126754 0.559558493817 -0.0610003119786 0.124733336811 0.524834090871 -0.0198432150667 0.61249560554 -20.530115848 2.0404749777 39.9437786923 25 0.705828895968 -0.108978646182 -0.884966271767 0.840946769767 0.0493291974753 2.11435394347 -0.225800211695 0.221986857156 0.13445417362 -0.107222294481 0.181676401537 0.0322605586428 -0.178865388253 -0.125042434132 0.0671677101336 0.419146092776 -0.0897051038726 -0.0175347394853 0.493334962641 0.0387526475073 0.499040589081 -14.4581703307 3.84400088368 33.7313785727 26 0.584442263001 0.0850832078604 -0.632161592226 2.14400405833 1.58610107771 1.90371688253 -0.27369744314 0.688443148732 0.56697121069 -0.493834340475 -0.423551917028 -0.0208882283631 -1.91490029691 0.575950908103 0.403033398543 0.947091095235 -0.189897074298 -0.120410643734 0.639198727219 0.12036168457 0.567386331066 -12.3671486226 6.46907181199 21.8522106764 27 3.18947374343 0.203023778169 -1.60070598081 5.66952261279 0.991846079052 2.95355316012 0.011925763163 0.726050776476 -0.00466306439695 -0.613492622565 -0.139150641089 0.257705110272 0.17731988819 -0.568648790233 0.030953227551 0.466238846114 -0.105450279319 0.00143665130853 0.645833488855 -0.0435196664719 0.476703571367 -18.6804069324 1.345140571 27.7969505492 28 1.89199548097 2.41205139628 -0.413475039715 1.88273617424 -1.28085595724 -0.652191912495 0.00821569945527 0.133330480182 0.012888589793 -0.190464680654 -0.0520405771683 0.263325623629 0.148965177926 0.030177088046 0.0544801984725 0.446896809185 -0.0659147975033 0.018397360681 0.495282995153 0.00889715442771 0.447898616307 -10.0750542343 7.15925262689 32.6814145403 29 3.99204767586 1.23457680762 2.04769634516 2.74179521311 -1.31237754633 2.84472377772 0.576856402613 -0.300913124982 -2.21452484993 0.563820170218 -0.783403140936 0.284172411031 1.14860655622 0.194441997362 0.252129836865 0.6527211704 -0.100922872828 0.0762266606772 0.511829276039 0.0309363606141 0.762958139373 -15.9298946238 -10.8170103211 42.2754957718
Refinement TLS group Show large table (4 x 29) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid -2 through 5 ) 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 6 through 11 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 12 through 22 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 23 through 31 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 32 through 57 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 58 through 66 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 67 through 86 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 87 through 95 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 96 through 109 )10 X-RAY DIFFRACTION 10 chain 'A' and (resid 110 through 114 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 0 through 10 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 11 through 23 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 24 through 57 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 58 through 71 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 72 through 86 )16 X-RAY DIFFRACTION 16 chain 'B' and (resid 87 through 109 )17 X-RAY DIFFRACTION 17 chain 'B'