Software Name Version Classification PHENIX1.17.1_3660refinement XDSdata reduction Aimlessdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 6TH5Resolution : 1.87→46.25 Å / SU ML : 0.2626 / Cross valid method : FREE R-VALUE / σ(F) : 1.35 / Phase error : 28.4735 Rfactor Num. reflection % reflection Rfree 0.2684 1638 5 % Rwork 0.2047 - - obs 0.2079 32749 99.33 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 ÅDisplacement parameters Biso mean : 42.66 Å2 Refinement step Cycle : LAST / Resolution : 1.87→46.25 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 3448 0 44 118 3610
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.0161 3634 X-RAY DIFFRACTION f_angle_d1.413 4937 X-RAY DIFFRACTION f_chiral_restr0.0639 555 X-RAY DIFFRACTION f_plane_restr0.0084 645 X-RAY DIFFRACTION f_dihedral_angle_d26.0091 503
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.87-1.92 0.3232 135 0.3105 2548 X-RAY DIFFRACTION 97.85 1.92-1.99 0.3494 135 0.2866 2570 X-RAY DIFFRACTION 99.82 1.99-2.06 0.3134 137 0.2665 2604 X-RAY DIFFRACTION 99.75 2.06-2.14 0.3044 135 0.2634 2562 X-RAY DIFFRACTION 99.7 2.14-2.24 0.3308 136 0.2387 2587 X-RAY DIFFRACTION 99.89 2.24-2.35 0.2931 137 0.228 2588 X-RAY DIFFRACTION 99.78 2.35-2.5 0.3062 136 0.2254 2601 X-RAY DIFFRACTION 99.67 2.5-2.69 0.2598 136 0.2238 2590 X-RAY DIFFRACTION 99.6 2.69-2.96 0.2799 136 0.2214 2594 X-RAY DIFFRACTION 99.56 2.97-3.39 0.2757 137 0.1987 2605 X-RAY DIFFRACTION 99.28 3.39-4.28 0.24 137 0.1609 2597 X-RAY DIFFRACTION 98.74 4.28-46.25 0.2192 141 0.1648 2665 X-RAY DIFFRACTION 98.42
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 19) 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 0.293652833442 -0.115505559974 0.194670191802 0.775103469635 -0.271589715536 0.614386015045 0.00343258959743 0.154489364672 0.137843900844 0.103223928381 -0.0510181576767 -0.0631776595472 -0.177196388519 0.0544857948232 -0.0102140669739 0.458589508118 0.346540802961 0.00887086979888 0.713740223412 0.581519306108 0.161509207736 16.8722848688 12.7120169208 11.5727298654 2 2.5271714381 -0.6018512422 -0.273725166933 1.86195306291 -0.156507599112 1.24717194508 -0.178405794024 0.46857350481 0.0045758563908 -0.451235829914 0.163325381813 0.25623261836 0.0863948639776 -0.191819572626 -0.0487491275472 0.45224757802 0.112130820833 0.011087393446 0.777678392176 0.123768093779 0.259453610262 17.9197979136 1.64455843055 0.975043101543 3 2.81837519533 0.0994339133808 0.271787237573 0.913051738542 -0.317794339098 0.950114726795 0.11127529872 0.534367422333 0.0234954557616 0.00528429354619 -0.0274637578079 -0.0856180618473 -0.103910301016 0.00695644331042 -0.113178523708 0.213056359696 0.0557851075704 -0.0140088446978 0.171165398755 -0.00755674360626 0.203980981502 21.7735430708 -3.86465442885 19.7272812646 4 1.43924051937 0.911433148054 -0.384568434069 1.40006356734 -1.1169785958 1.0310415569 -0.193707740218 0.103731756261 -0.28758096072 0.3633024864 0.21110019921 -0.179581400389 0.0875467950428 -0.0624508080635 0.0434311233379 0.313846349267 0.0497866768997 -0.0168105135908 0.158227778273 -0.00110380126519 0.271644843974 19.6639507869 -14.9660184433 27.7428717026 5 1.86793481178 1.43047897953 0.102957921098 2.04777764172 0.648951485709 2.06942745369 0.147521136228 -0.0736106137359 -0.0536674146002 0.435090947543 0.0586327473748 -0.210466861883 -0.199952981648 0.208528191141 0.0229271872387 0.352636939013 -0.014210795756 -0.0411221992915 0.0714763484983 0.0244552199179 0.310032933917 31.0066653685 -8.63478788773 33.3671465008 6 0.996425811856 -0.0527200387921 0.268518303153 1.33735015952 0.414331079225 0.804463774152 0.109188643442 -0.0374340373069 0.0903329159612 0.675590194416 -0.212615450049 -0.124686492325 0.0230472907235 0.272901730223 0.0875332179163 0.293187887938 -0.0136599540123 0.0171492140239 0.16052136963 -0.0115899379976 0.301987851216 33.4423547836 -1.72172711404 29.3619537794 7 0.267854933469 0.0489469379209 0.527526038147 0.792873154238 -0.0535283830563 1.17974298335 0.120413576182 1.04032268267 -0.1751897365 -0.4042444688 -0.110935097795 -0.460574527282 -0.211691166409 0.332916714694 0.0509937080236 0.321725826938 0.074919956512 0.110052869253 0.762961546737 -0.026973723433 0.342847936203 37.4986007587 -1.44410934034 9.5339771552 8 1.43585515619 0.24001457548 0.321496959031 0.556614441981 -0.705570644627 1.4877124082 0.0959204852108 0.805283832931 0.206058215957 -0.0215064957391 -0.0311575858752 -0.0765937846383 -0.210832001251 0.0453191420611 -0.00117724984102 0.239319071985 0.0968846156745 0.0920804501408 0.365726055471 0.0666433799814 0.329663497877 29.727235974 2.7177665585 14.5274976625 9 0.535588664666 0.0935281519199 -0.0569014255074 0.386066964292 -0.394043138354 0.495084039878 0.116807482211 0.921928727329 0.653083573061 -0.184247866702 -0.0562014412862 -0.0215338290444 -0.189143636362 0.209768327027 0.0347872411152 0.302576419962 0.039233620982 0.0477771349155 0.484763067345 0.179746380373 0.333669590604 25.5375988991 7.30640084174 11.7652060555 10 2.62224016588 0.533287617417 0.138959709705 0.625338303295 -0.11702904069 2.40143882157 0.300453519907 0.434053528249 0.25707847715 -0.0457086776765 -0.339005336588 -0.259476214169 -0.276624979524 0.245569765481 -0.0202221978019 0.253780691568 0.00466706592656 0.0631098794482 0.254243102751 0.0744701690119 0.314575454059 37.9927398681 1.53268898203 19.7271069359 11 0.364013557332 -0.0595817161209 -0.0819536525432 0.962109170339 -0.112355673888 0.635384381962 -0.0715003691307 0.213048782354 -0.236692156573 0.187059085095 -0.101669190839 0.179489500978 0.374501360187 -0.0860206009673 -0.181835289688 0.470713888695 0.123689830133 -6.5755731098E-5 0.657727742422 -0.54874428227 0.524146656917 11.2582835275 -19.925739996 11.6212327817 12 1.02981324248 0.543173227708 -0.386556732678 0.827415267279 0.376299821803 1.01020533823 0.12885474839 0.833268110909 -0.0583906026044 -0.214065574169 -0.175825824882 0.101269983641 0.1593032646 0.00182687428819 -0.0236925861634 0.280299178671 0.115187128174 -0.0188026055519 0.463052538993 -0.0187043171304 0.225191476942 7.75058643627 -4.71389965508 14.4716247766 13 1.97830844467 0.729086853123 -0.278844449004 0.407293390354 0.278992078876 1.12769517884 -0.10197581242 0.343082864332 0.221872763641 0.206232762687 0.109123197722 0.0184552936828 -0.151048186598 0.104053284301 0.0434248306821 0.291869011436 0.0517462745587 0.0121083837014 0.140556372898 0.0278995391447 0.284390337502 7.43304927633 7.11750431888 28.9896109915 14 1.25262103639 0.147703973828 -0.134899200345 1.59058509118 -0.165239017454 1.09729251529 0.0492251080993 -0.0274711885694 0.0504987729459 0.494601960531 -0.0284197280317 0.147144598901 -0.0725256637049 -0.139717919523 0.0155843961439 0.286341369585 -0.00824456113337 -0.0215639165997 0.172292660558 -0.00473133893851 0.276069831698 -4.84753925165 -3.16726672054 30.8919801319 15 0.0750902474455 0.172287429683 -0.085795051095 0.569298695022 -0.241968620527 0.113031217894 0.126606828595 0.7342555716 -0.155462190026 -0.185385307967 0.0801069770324 0.380314256566 0.120844704982 -0.198864339373 0.132456421785 0.248686897813 0.0644042679835 -0.188142424966 1.07439399418 -0.0767022152289 0.291506119634 -9.06734286749 -5.66562646774 9.83853362227 16 2.53123373212 0.349346822365 -0.349119568622 1.29592889994 0.834325458628 1.58079448002 0.0695242439694 1.00932762106 -0.239506432779 -0.0129005858872 0.0147597914381 0.138046765794 0.138488083297 -0.0877371954271 -0.0410366834372 0.184983073355 0.073341081002 -0.052780234239 0.431516632697 -0.0822565407875 0.238127460816 -1.10147981667 -9.76073988417 14.6411085155 17 1.1866233897 -0.198661096017 -0.19385015131 1.0054892225 1.08978198997 1.76535428926 0.0550984806324 0.886271212965 -0.46652675996 -0.0888948373127 -0.0222350506921 0.0117629510723 0.163798118167 0.0555147115467 0.0535743509616 0.215219790724 0.0292698345252 -0.0538009388992 0.432847697091 -0.189618257351 0.280777806803 2.21066147654 -14.1660866825 15.1606776299 18 1.32899687475 0.203121517933 0.45701480857 0.165226610501 0.0298082855295 0.157741323364 0.0340961968646 1.49978750352 -0.367243665029 -0.445733874849 -0.208160648996 -0.0907560850864 -0.0028127552697 -0.407151924023 -0.144521166775 0.371758756581 0.0317605231565 -0.0757005788728 0.824740478901 -0.370312640112 0.295168340387 3.22714449722 -14.6137893205 11.0569817026 19 2.24419195176 0.177371935804 0.172538062225 2.14649238385 0.0962406172294 2.3881021686 0.1776428686 0.688592243572 -0.12082164988 -0.0547377125504 -0.304191084496 0.0410960221398 0.117040561159 -0.265436541943 0.0370691678169 0.177673011196 0.022887437704 -0.0286853575325 0.424497129398 -0.0678045810713 0.364632350231 -9.14356207984 -7.9816763356 19.574340086
Refinement TLS group Show large table (4 x 19) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 25 through 38 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 39 through 51 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 52 through 81 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 82 through 101 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 102 through 114 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 115 through 135 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 136 through 161 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 162 through 176 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 177 through 221 )10 X-RAY DIFFRACTION 10 chain 'A' and (resid 222 through 241 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 25 through 38 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 39 through 82 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 83 through 106 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 107 through 135 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 136 through 161 )16 X-RAY DIFFRACTION 16 chain 'B'