| Software | | Name | Version | Classification |
|---|
| XDS | | data reduction| Aimless | 0.8.2data scaling| PHASER | 2.8.3phasing| PHENIX | 2.0_5936refinement Coot | 0.9.8.95| model building | | | | | | | | |
|
|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→45.36 Å / SU ML: 0.3421 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.871 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
|---|
| Rfree | 0.2301 | 3619 | 5.05 % |
|---|
| Rwork | 0.2 | 67993 | - |
|---|
| obs | 0.2016 | 71612 | 97.82 % |
|---|
|
|---|
| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
|---|
| Displacement parameters | Biso mean: 60.82 Å2 |
|---|
| Refinement step | Cycle: LAST / Resolution: 2.75→45.36 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
|---|
| Num. atoms | 16690 | 0 | 136 | 133 | 16959 |
|---|
|
|---|
| Refine LS restraints | | Refine-ID | Type | Dev ideal | Number |
|---|
| X-RAY DIFFRACTION | f_bond_d| 0.0031 | 17146 | | X-RAY DIFFRACTION | f_angle_d| 0.5505 | 23325 | | X-RAY DIFFRACTION | f_chiral_restr| 0.0446 | 2682 | | X-RAY DIFFRACTION | f_plane_restr| 0.0047 | 3053 | | X-RAY DIFFRACTION | f_dihedral_angle_d| 15.6678 | 6221 | | | | | |
|
|---|
| LS refinement shell | | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
|---|
| 2.75-2.79 | 0.3362 | 144 | 0.2981 | 2598 | X-RAY DIFFRACTION | 97.68 | | 2.79-2.82 | 0.3368 | 124 | 0.2803 | 2625 | X-RAY DIFFRACTION | 97.52 | | 2.82-2.86 | 0.3191 | 144 | 0.2818 | 2590 | X-RAY DIFFRACTION | 97.57 | | 2.86-2.91 | 0.3016 | 145 | 0.2794 | 2624 | X-RAY DIFFRACTION | 97.67 | | 2.91-2.95 | 0.3206 | 137 | 0.2883 | 2514 | X-RAY DIFFRACTION | 96.72 | | 2.95-3 | 0.2888 | 113 | 0.2854 | 2477 | X-RAY DIFFRACTION | 91.36 | | 3-3.05 | 0.3212 | 145 | 0.2874 | 2512 | X-RAY DIFFRACTION | 95.37 | | 3.05-3.11 | 0.3521 | 149 | 0.2661 | 2614 | X-RAY DIFFRACTION | 98.78 | | 3.11-3.17 | 0.2977 | 116 | 0.2588 | 2679 | X-RAY DIFFRACTION | 98.8 | | 3.17-3.23 | 0.3104 | 142 | 0.2464 | 2622 | X-RAY DIFFRACTION | 98.75 | | 3.23-3.3 | 0.2869 | 145 | 0.237 | 2631 | X-RAY DIFFRACTION | 98.83 | | 3.3-3.38 | 0.2578 | 138 | 0.2275 | 2632 | X-RAY DIFFRACTION | 98.79 | | 3.38-3.46 | 0.3319 | 131 | 0.2833 | 2608 | X-RAY DIFFRACTION | 97.86 | | 3.46-3.56 | 0.2331 | 124 | 0.2156 | 2638 | X-RAY DIFFRACTION | 98.78 | | 3.56-3.66 | 0.2743 | 151 | 0.2275 | 2622 | X-RAY DIFFRACTION | 98.44 | | 3.66-3.78 | 0.2712 | 126 | 0.2082 | 2654 | X-RAY DIFFRACTION | 98.55 | | 3.78-3.92 | 0.2529 | 134 | 0.2322 | 2610 | X-RAY DIFFRACTION | 97.72 | | 3.92-4.07 | 0.2175 | 151 | 0.1824 | 2621 | X-RAY DIFFRACTION | 98.37 | | 4.07-4.26 | 0.2037 | 148 | 0.1619 | 2596 | X-RAY DIFFRACTION | 98.6 | | 4.26-4.48 | 0.161 | 141 | 0.1516 | 2664 | X-RAY DIFFRACTION | 98.66 | | 4.48-4.76 | 0.1817 | 151 | 0.1464 | 2623 | X-RAY DIFFRACTION | 98.61 | | 4.76-5.13 | 0.1919 | 127 | 0.16 | 2648 | X-RAY DIFFRACTION | 98.47 | | 5.13-5.65 | 0.2012 | 148 | 0.164 | 2604 | X-RAY DIFFRACTION | 97.11 | | 5.65-6.46 | 0.1919 | 138 | 0.1755 | 2567 | X-RAY DIFFRACTION | 95.41 | | 6.46-8.13 | 0.1784 | 149 | 0.1625 | 2697 | X-RAY DIFFRACTION | 99.65 | | 8.13-45.36 | 0.1571 | 158 | 0.1418 | 2723 | X-RAY DIFFRACTION | 99.17 |
|
|---|
| Refinement TLS params. | Method: 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) |
|---|
| 1 | 3.1918558472545 | -0.76690396910483 | 0.22645218319209 | 2.4583339225369 | 0.175683930834 | 1.6121445377643 | 0.025138784502174 | 0.094791365620739 | -0.30282121903856 | 0.20316675675518 | 0.11699493920924 | 0.020437997468639 | 0.08675973134816 | 0.0014668672779027 | -0.13580450457918 | 0.2755046586865 | -0.04832209949729 | 0.019346934739113 | 0.202734856337 | 0.012845975446868 | 0.25277017752996 | -5.466117746767 | -21.357419033465 | 48.215056313617 | | 2 | 1.7531036408584 | -0.20490252699141 | 0.72873483133463 | 4.1867183990084 | -0.64917858756995 | 0.84578475874749 | -0.15102189787422 | 0.22409573191376 | 0.55141279386888 | 0.18126992616393 | -0.017604301771551 | -0.18077148522763 | -0.26666515595371 | 0.1337772494543 | 0.12384311216903 | 0.37448599280356 | -0.014705881516626 | 0.052527518864725 | 0.35723808070938 | 0.010470120407935 | 0.38781340050169 | 10.387369631965 | 6.3394693907356 | 41.99189551699 | | 3 | 1.7311104921895 | 0.010256508128093 | -0.13533211094061 | 1.3116102982718 | 0.23605899623058 | 0.54316957508255 | -0.026527534241825 | 0.0016723137010581 | 0.38513843866323 | 0.14798614655856 | -0.096429947621469 | -0.236063925402 | -0.15922694500546 | 0.051069960136657 | 0.069211856466195 | 0.47050455163056 | -0.056313340876349 | -0.00060935887297742 | 0.27700907199109 | 0.073678810925716 | 0.40673569880654 | 9.9005263310929 | 13.996041698058 | 40.766638675221 | | 4 | 1.8440281192234 | -0.069184697743725 | 0.30480892955674 | 4.4198986421504 | -1.4443181284493 | 0.62672776808311 | -0.18070416512118 | 0.047260751213746 | 0.42026931928506 | 0.3574123581706 | 0.12365370788198 | 0.061948294000511 | -0.54628266754295 | 0.066736433989251 | 0.05807638473591 | 0.46342129353027 | -0.029400827187159 | 0.0022935041724427 | 0.33568843881359 | 0.018299867629892 | 0.3989795776906 | -10.757139974331 | 8.2342243052609 | 46.524010866109 | | 5 | 2.3860122777287 | 0.19926611829412 | 0.6825438490919 | 2.8795754825695 | 0.81773818221849 | 2.2298094191476 | 0.044380974783005 | 0.42409684015165 | 0.36280434601694 | -0.31357153945837 | 0.012482672403962 | 0.28246699746626 | -0.35947181137607 | -0.017618904722699 | -0.1011919189436 | 0.40106349373494 | 0.020079565339526 | 0.01597325993575 | 0.29597871795222 | 0.065782075994055 | 0.51687379067308 | -22.160667934623 | 3.572724073446 | 41.088751573237 | | 6 | 2.1282861703675 | -0.56707392489172 | -1.059304014601 | 4.3026577754293 | -1.3889970330469 | 8.1729948147721 | -0.052714718504499 | 0.12718948998258 | 0.25285551175271 | -0.01471338122167 | -0.11313101682816 | 0.20492258043807 | -0.6358201423291 | 0.36534976109388 | 0.092244889233933 | 0.30230934582681 | -0.0028043684007577 | -0.082829051732875 | 0.38766270231652 | 0.041803882654388 | 0.52241628608286 | -17.240615976548 | 15.535324827407 | 43.120880797299 | | 7 | 2.9200966264509 | 0.091022227542156 | -0.38799867085842 | 1.8199355175678 | 0.26053545954075 | 1.0550373898068 | 0.05911838261419 | 0.73611561246755 | 0.029778833725896 | -0.22233673462913 | 0.092205879911923 | 0.1496073499783 | -0.1371061170555 | 0.10974060099088 | -0.13710218083946 | 0.28875070568278 | -0.024515375207136 | -0.012593437610635 | 0.43931320706378 | 0.042826709784561 | 0.28730218317287 | -15.117116702258 | -12.26634969678 | 20.552740115559 | | 8 | 1.1625411112329 | -0.25415889709014 | 0.30282973326264 | 0.33782747126098 | 0.18214714894228 | 1.0618229628582 | 0.111342686302 | 0.53314754847678 | -0.7046103481161 | -0.099970475575612 | -0.10459689020416 | -0.061254313762239 | 0.21915148663993 | -0.041028519035681 | 0.028024404336669 | 0.45740059743853 | -0.0030639417692818 | -0.1050793674501 | 0.64272109674676 | -0.23906241548683 | 0.76137968982082 | -24.85122983824 | -37.357478247177 | 16.209459257803 | | 9 | 2.2950545446082 | 0.083380765792035 | -0.69494907689254 | 2.0015257108472 | 1.2416970309369 | 2.5328980644309 | 0.084641501733956 | 0.10599104114778 | -0.52068508635556 | -0.029745884683703 | 0.012186480027316 | 0.71026841622113 | 0.2523723850053 | -0.24635254165936 | -0.16272440672906 | 0.38626602554547 | -0.056564656384945 | -0.11230885497627 | 0.42630679396751 | -0.042076375869215 | 0.84351875736676 | -29.768380658684 | -43.101248740799 | 30.509189463483 | | 10 | 1.7778134196046 | 0.24389327610887 | 0.073281004795872 | 1.6548571490821 | 0.51913663181348 | 1.2357209597671 | 0.18160948586996 | 0.065563377658958 | -0.47880992412003 | 0.067302673576212 | 0.11965546744182 | 0.23342112956197 | 0.32381111883385 | -0.26828296940661 | -0.23131710242671 | 0.36459415978919 | -0.072960734231975 | -0.076941113957759 | 0.42190822441169 | 0.060809802317729 | 0.55834224626382 | -37.868346858375 | -31.938805877217 | 35.104794407247 | | 11 | 5.554602636394 | 1.889874685783 | 0.20183487947732 | 0.87527142232565 | 0.71256734784208 | 2.0497476517156 | 0.26198248773884 | -0.44079454230408 | -0.51480304069967 | 0.25511291538032 | -0.10732831919899 | -0.032474891930099 | 0.35605195161286 | -0.033616868998802 | -0.080925725205159 | 0.32978175906679 | -0.011225779957443 | 0.030788273915519 | 0.32823662809492 | 0.019224836321844 | 0.43593601603408 | -29.964623206504 | -17.122615243207 | 43.650144811746 | | 12 | 2.0248680332001 | 1.3605369991351 | 0.73610224349803 | 5.4027665679381 | -2.0734433556486 | 2.8613173871998 | 0.32340166535904 | -0.18681417865451 | -0.13628284476491 | 0.18687891934238 | -0.26651350441362 | 0.017295284068837 | 0.20171339929902 | -0.1671527358477 | -0.094017653633871 | 0.32695681227682 | 0.0092071543881122 | 0.10791726570148 | 0.38004571487761 | -0.013927623337723 | 0.38565763927537 | -37.958206477782 | -19.258051662452 | 48.768911378615 | | 13 | 2.4698809746951 | -0.3754070093706 | -0.030637365938924 | 1.3357451969858 | 0.19357724961544 | 2.865258847404 | 0.11634405214883 | 0.67296394746527 | 0.084380519872962 | -0.20579873802689 | -0.036127502362195 | -0.09738591870006 | -0.034712388500398 | 0.29666089123707 | -0.10769321304684 | 0.32193110057471 | 0.0011761424652716 | 0.022095628873272 | 0.58047446130366 | -0.039946565966223 | 0.31345799696295 | 16.574172102816 | -17.010194570822 | 17.96863000001 | | 14 | 2.0740400387644 | -1.0248861464473 | 2.2944265530763 | 1.1168664197334 | -1.2973061645379 | 3.2044359798802 | -0.0098589328514619 | 0.2756429620823 | 0.29963789876965 | 0.28002189918294 | 0.054565352013601 | 0.0028513793678599 | -0.41727189848222 | 0.58838424037153 | -0.0060831347681962 | 0.39061940720025 | -0.034882611461853 | -0.012147846695143 | 0.41271948660445 | -0.060029236731393 | 0.55394141744783 | 24.945425649074 | -12.104300084733 | 43.391187425814 | | 15 | 5.4941636922334 | -1.5239684369769 | -0.067171192770763 | 4.1157136084101 | 0.18142682237027 | 3.6183777786564 | 0.0016306934713563 | 0.25970413991109 | -0.22542717753725 | 0.1103934521746 | 0.13137054732183 | -0.49005170812708 | 0.063544100034179 | 0.37095759150032 | -0.073305669902505 | 0.28296281206556 | 0.039448395611151 | -0.041965575513101 | 0.31742448709734 | -0.059546822715966 | 0.41829525361868 | 32.305823574309 | -27.188559696964 | 49.14053500178 | | 16 | 4.330498978628 | -2.6920719611651 | -1.0384314950678 | 3.3663496751584 | -0.95900627745893 | 2.1825348597044 | -0.18468194163175 | -0.077981703344413 | -0.063265383792676 | 0.089050873683016 | 0.12808203710337 | -0.31573895428787 | 0.062776870557798 | 0.072057190535198 | 0.12323007400681 | 0.3340254370462 | -0.03973846832901 | -0.045718547191188 | 0.31458706531299 | -0.056132507911564 | 0.31029804812971 | 24.40113543148 | -20.521278677457 | 53.77510581017 | | 17 | 2.4640492298022 | 0.02874042585207 | 0.37433277616362 | 1.1733644520066 | 0.22905001054742 | 4.3105960203238 | -0.10043596585892 | 0.5953833882812 | -0.41405012769654 | 0.067740919086064 | 0.048805957784093 | -0.47623869015561 | 0.31359697299204 | 0.58729593052756 | 0.029831054359662 | 0.37486211494718 | 0.025095747248323 | -0.021410424068797 | 0.46493910740084 | -0.088154326446929 | 0.66562041373288 | 43.653260833608 | -41.590898277081 | 42.679841132105 | | 18 | 2.8925507433948 | -1.9549237996152 | -0.053477979862231 | 2.1702890477135 | -1.0505616500352 | 1.5659593278468 | 0.37167538937472 | 0.39232264203611 | -0.34736634122816 | 0.08806837129303 | -0.47194928698851 | 0.097408472788835 | -0.05211710522933 | 0.043911881708982 | 0.13677832583004 | 0.35107474140718 | -0.0078407033857117 | -0.051087292086483 | 0.43297741710884 | -0.18074324074551 | 0.46821918764061 | 32.764136057259 | -33.804967707969 | 34.829383523996 | | 19 | 1.7853693799226 | -1.1526151863688 | 0.31621978156071 | 2.165201403926 | -0.63213396622852 | 0.95855303371626 | 0.21468010964537 | 0.47471694961166 | -0.50681428221076 | -0.18495566522909 | -0.14164626667963 | 0.097259413279369 | 0.24179797115971 | 0.27323825535698 | -0.13113079277738 | 0.35809983281185 | 0.038799623847412 | -0.033869508539209 | 0.66185261642638 | -0.24275249712134 | 0.53473863275884 | 29.96053798028 | -39.433074012402 | 24.667169712437 | | 20 | 2.1945888308826 | -0.28781898711286 | 0.14959445950995 | 1.4369997920537 | -1.143449713693 | 1.7690284243956 | 0.30862018603141 | 0.66069574851019 | -0.55060168632559 | 0.016412932794248 | -0.18067437633733 | -0.21661747668934 | 0.239305598684 | 0.3385351038545 | -0.043074611376552 | 0.45940838119201 | 0.050733979182917 | 0.081812453120457 | 0.60072598617407 | -0.33551517838894 | 0.71616603377146 | 40.153602256857 | -44.737740307577 | 27.887597579169 | | 21 | 1.7593076645465 | -0.40732436682538 | -0.46556996609542 | 0.53941908626723 | -0.18649854646648 | 2.5946903829662 | 0.11756107363432 | 0.35986391347015 | -0.56927917321289 | -0.11425050155376 | -0.022505504304003 | 0.040347216109959 | 0.27627707395878 | -0.044587217532051 | -0.078006822138371 | 0.4256093054236 | 0.043408512013767 | -0.088702640693265 | 0.40134398031219 | -0.21424732057168 | 0.59586320989202 | 4.5930357224845 | -43.648094005979 | 27.499188004373 | | 22 | 1.0991007046676 | -0.0076690813920977 | 0.49791437247104 | 0.30980540849793 | 0.30116672253076 | 1.0447429301133 | 0.28466263204828 | 0.7937290131995 | -0.52912661108904 | -0.17339403099792 | -0.11308466164574 | 0.18256137704983 | 0.39030901158978 | 0.28322739749492 | -0.21501474677718 | 0.61037284865078 | 0.11444700106775 | -0.16907915935324 | 0.9476486324312 | -0.40998402971518 | 0.84206244922918 | -13.767877150981 | -42.664528570718 | 7.18937741894 | | 23 | 0.89458310433088 | -0.30675526068564 | -0.5480324872292 | 1.0645465080419 | 1.3616750897325 | 2.310397148425 | 0.17687736841732 | 1.4274149761978 | -0.45939291096711 | -0.41848661387658 | 0.017416427313772 | 0.097241833178617 | 0.19118256838632 | 0.055558301458669 | -0.055813130276995 | 0.6376075811256 | 0.15551540235331 | -0.11871451127279 | 1.2355628531404 | -0.41043449646945 | 0.62315660643654 | -9.4203298584329 | -34.685542375447 | -5.0559367142461 | | 24 | 0.50798919596223 | -0.070130146870714 | -0.062246553035083 | 0.58408882347144 | 0.39450372132107 | 1.7447448275818 | 0.11998261343284 | 0.90563027150051 | -0.36838501353731 | -0.37458834629254 | -0.061825903080054 | -0.0910152341793 | 0.11580546059069 | 0.021826527931169 | -0.10144440965042 | 0.69907423950729 | 0.16395986421838 | -0.042490148551813 | 1.3336239287117 | -0.49839556050493 | 0.65159288478798 | 10.274727253942 | -42.285583616067 | -6.1449100557373 | | 25 | 0.64226678591818 | 0.4844479701124 | -0.18588284376551 | 1.2540232695641 | -0.75810887029819 | 2.2917588231662 | 0.10794993333937 | 0.80337119862847 | -0.11664448025199 | -0.11541676905176 | 0.014677652012023 | -0.083811648537283 | 0.10002192059284 | 0.32933142343442 | -0.13664785630051 | 0.54479457960595 | 0.14048800011697 | 0.010924696826723 | 1.0425463920911 | -0.384053085569 | 0.63324636462829 | 21.953812291273 | -39.112959247198 | -0.53537870171458 |
|
|---|
| Refinement TLS group | Refine-ID: X-RAY DIFFRACTION | ID | Refine TLS-ID | Selection details | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
|---|
| 1 | 1 | chain 'A' and (resid 6 through 173 )AA| 6 - 173 | 1 - 168 | | 2 | 2 | chain 'A' and (resid 174 through 304 )AA| 174 - 304 | 169 - 299 | | 3 | 3 | chain 'A' and (resid 305 through 365 )AA| 305 - 365 | 300 - 360 | | 4 | 4 | chain 'A' and (resid 366 through 440 )AA| 366 - 440 | 361 - 435 | | 5 | 5 | chain 'A' and (resid 441 through 520 )AA| 441 - 520 | 436 - 515 | | 6 | 6 | chain 'A' and (resid 521 through 559 )AA| 521 - 559 | 516 - 554 | | 7 | 7 | chain 'B' and (resid 6 through 173 )BF| 6 - 173 | 1 - 168 | | 8 | 8 | chain 'B' and (resid 174 through 220 )BF| 174 - 220 | 169 - 215 | | 9 | 9 | chain 'B' and (resid 221 through 317 )BF| 221 - 317 | 216 - 312 | | 10 | 10 | chain 'B' and (resid 318 through 440 )BF| 318 - 440 | 313 - 435 | | 11 | 11 | chain 'B' and (resid 441 through 488 )BF| 441 - 488 | 436 - 483 | | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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