Software | Name | Version | Classification |
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PHENIX | 1.20.1_4487refinementHKL-3000 | | data reductionHKL-3000 | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→29.66 Å / SU ML: 0.1964 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.554 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1658 | 1990 | 1.34 % | random |
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Rwork | 0.1446 | 147036 | - | - |
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obs | 0.1449 | 149026 | 98.65 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 35.47 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.59→29.66 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 7759 | 0 | 267 | 853 | 8879 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0081 | 8196 | X-RAY DIFFRACTION | f_angle_d1.0189 | 11132 | X-RAY DIFFRACTION | f_chiral_restr0.0549 | 1302 | X-RAY DIFFRACTION | f_plane_restr0.0081 | 1419 | X-RAY DIFFRACTION | f_dihedral_angle_d13.4351 | 2933 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.59-1.63 | 0.3377 | 130 | 0.3216 | 9657 | X-RAY DIFFRACTION | 91.3 | 1.63-1.67 | 0.2951 | 139 | 0.2734 | 10272 | X-RAY DIFFRACTION | 97.14 | 1.67-1.72 | 0.2739 | 140 | 0.2362 | 10440 | X-RAY DIFFRACTION | 98.13 | 1.72-1.78 | 0.2329 | 142 | 0.2023 | 10449 | X-RAY DIFFRACTION | 98.39 | 1.78-1.84 | 0.2062 | 142 | 0.1864 | 10468 | X-RAY DIFFRACTION | 98.89 | 1.84-1.91 | 0.2127 | 141 | 0.1864 | 10519 | X-RAY DIFFRACTION | 98.93 | 1.91-2 | 0.2173 | 142 | 0.156 | 10502 | X-RAY DIFFRACTION | 99.23 | 2-2.11 | 0.1495 | 144 | 0.1478 | 10575 | X-RAY DIFFRACTION | 99.56 | 2.11-2.24 | 0.189 | 143 | 0.1379 | 10625 | X-RAY DIFFRACTION | 99.72 | 2.24-2.41 | 0.155 | 144 | 0.1345 | 10614 | X-RAY DIFFRACTION | 99.81 | 2.41-2.65 | 0.1841 | 145 | 0.1331 | 10652 | X-RAY DIFFRACTION | 99.94 | 2.65-3.04 | 0.1846 | 146 | 0.1379 | 10721 | X-RAY DIFFRACTION | 99.99 | 3.04-3.82 | 0.1518 | 145 | 0.1326 | 10692 | X-RAY DIFFRACTION | 100 | 3.82-29.66 | 0.1196 | 147 | 0.1259 | 10850 | X-RAY DIFFRACTION | 99.94 |
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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) |
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1 | 2.76315658645 | -1.23940019483 | 0.483164042926 | 3.26808254417 | -0.390099112249 | 2.63662907925 | 0.00784249024361 | 0.294700053627 | 0.075445572949 | -0.162144136561 | 0.0282932564721 | 0.0895927350906 | -0.271154600892 | 0.0218852161739 | -0.0694888527992 | 0.395926336464 | -0.0870586527261 | -0.00695195823445 | 0.279795988857 | 0.0305507210349 | 0.171635548784 | -33.0220133332 | 16.7774721096 | 11.1712966997 | 2 | 6.89411148281 | -3.05653514131 | 1.89924474921 | 2.25137313341 | -1.12767568932 | 2.16900724362 | 0.0450959918685 | 0.336144458984 | -0.118816839194 | -0.250239653646 | -0.0503474023884 | 0.00446123151164 | -0.233173313836 | 0.0103891656884 | -0.00528905967747 | 0.503358490065 | -0.126802983737 | 0.00875918824158 | 0.351387974393 | 0.0604596930425 | 0.247000933985 | -30.3634387279 | 20.5405630559 | 7.84814149672 | 3 | 7.31184177905 | -4.93507243131 | -1.38425031784 | 7.32064998553 | 1.19658230748 | 1.73012029209 | -0.241830533441 | 0.319895296275 | 0.70377391277 | 0.370212441558 | 0.0531123630887 | -0.601588004861 | -0.776003866291 | 0.353349860786 | -0.0149882993212 | 0.62614056436 | -0.218543505959 | -0.0448941645647 | 0.383858009396 | 0.072607978594 | 0.338130729967 | -21.957140459 | 25.5991596047 | 16.8982996621 | 4 | 2.68249988091 | -2.59846960618 | -0.675340456597 | 3.88410190794 | 0.598745402716 | 1.39121186281 | -0.0262467337875 | 0.17331390478 | 0.0251610247278 | -0.193292857778 | -0.0202977597796 | -0.243886108779 | -0.202569987899 | 0.283114217878 | 0.158173224624 | 0.369891121955 | -0.126396723684 | 0.0449624112002 | 0.393602402962 | 0.00567925597796 | 0.254892833339 | -20.1577981547 | 6.40701048349 | 14.8569498788 | 5 | 1.94806595082 | -1.1487958012 | -0.688813290732 | 2.53562272885 | 0.784486429263 | 2.49838029834 | 0.0609119840142 | 0.252015587912 | 0.171358469368 | -0.225041803253 | -0.0951281468965 | -0.332259158725 | -0.532969792532 | 0.283907104051 | -0.0402164485426 | 0.442647171911 | -0.173804177704 | 0.00291697674421 | 0.350399994171 | 0.0349658619487 | 0.288142117075 | -18.7134376367 | 13.3642475514 | 22.0991311743 | 6 | 0.800213645911 | -0.294916435388 | -0.026828262081 | 1.23165866093 | -0.0933709813037 | 1.54000678928 | -0.0383577199983 | 0.149769888686 | -0.0312838708381 | -0.116619812737 | 0.0366086676279 | -0.0767035465075 | -0.200544865341 | 0.168727939648 | 0.0232715146264 | 0.297143470688 | -0.104652233821 | 0.0157649889876 | 0.266200460979 | -0.014042542077 | 0.207758022079 | -26.4154427716 | 4.32988338591 | 22.9125568899 | 7 | 7.10417227836 | -5.10104238018 | -5.4627965059 | 6.46177524185 | 5.61070813966 | 5.70924388485 | 0.225680348849 | 0.235035166315 | 0.0483314317171 | -0.942477409836 | 0.229152248152 | -0.340478908173 | -0.541977121381 | 0.733713043313 | -0.430877868631 | 0.536777791825 | -0.106493115173 | 0.042601072862 | 0.526647383746 | -0.06938320937 | 0.23337039385 | -22.9655904315 | -5.22774615938 | 0.909379672403 | 8 | 4.0815042872 | -0.473552081433 | -5.4338107934 | 6.28667491052 | -2.87283089998 | 9.41355540326 | 0.0620002648524 | 0.0685633225616 | -0.32717229889 | -0.242336766092 | -0.380474585002 | 0.221622593353 | 0.0557495751865 | -0.593630300288 | 0.307466884774 | 0.460111938757 | -0.0038069993417 | -0.0259929867644 | 0.459015258472 | -0.13089028619 | 0.276212084354 | -28.7652365867 | -11.9556925276 | 0.744715449099 | 9 | 0.71789954952 | -0.41210752152 | 0.152758877992 | 3.42271599491 | 0.988417984022 | 2.1530703546 | -0.0131452523418 | 0.145030199834 | -0.0301295391106 | -0.221384210554 | 0.0559348731817 | 0.0496691570026 | -0.105599237618 | -0.0524456025314 | -0.0496733400718 | 0.240498502322 | -0.0839991637766 | 0.0143784835161 | 0.277142445902 | -0.0137460262121 | 0.182976819088 | -35.9078126945 | 0.55221026278 | 19.2277833143 | 10 | 5.32848732187 | 0.32580066544 | -0.985927130315 | 2.67015743063 | 0.330598663888 | 4.93104246883 | -0.045771027467 | -0.0756534954085 | 0.120490533015 | -0.0660752527997 | 0.0236747297367 | 0.473584810563 | -0.217569344387 | -0.0496146615604 | -0.00969913015178 | 0.169613197176 | 0.0321773421886 | -0.0307104349763 | 0.28458834574 | 0.0533937498104 | 0.36567415941 | -58.7220876705 | 0.48456009857 | 30.5054161532 | 11 | 5.48565501434 | -5.56860644287 | 2.30551432923 | 9.33616689554 | -3.61994188459 | 3.09300820932 | 0.0273947445026 | -0.101466987561 | 0.0377261067641 | 0.0458457468512 | -0.018446910498 | 0.489378262017 | -0.146373865009 | -0.0433354970244 | -0.0295592424956 | 0.180088768586 | -0.000676126094315 | 0.019364345899 | 0.331998769326 | 0.0297102267976 | 0.409189635998 | -63.8924448802 | -1.03312994768 | 32.4699743776 | 12 | 2.8052431251 | -1.76703981904 | 2.87394362865 | 4.03732616265 | -3.19145939288 | 5.51757970537 | 0.110365851395 | 0.0934723771811 | -0.471243464566 | -0.502005715153 | 0.355012283938 | 0.779881926422 | 0.587532247545 | -0.550857384984 | -0.431701102105 | 0.295016579135 | -0.0942814356216 | -0.0190580796639 | 0.463076337368 | 0.064475797295 | 0.585249055029 | -63.8503582345 | -13.5930863892 | 28.0689737014 | 13 | 1.73070950274 | -0.668383309937 | 1.85115040323 | 1.34501640647 | -0.903315290887 | 3.67129979258 | -0.147179664553 | -0.237879074375 | -0.0863034639931 | 0.0601160092569 | 0.195535683855 | 0.186398811092 | -0.191128808606 | -0.446128474951 | -0.0151876058027 | 0.199856206009 | -0.014064996658 | 0.0385711726684 | 0.338880522547 | 0.0362357406381 | 0.308900200563 | -48.6575387456 | -9.77018368972 | 39.4354244071 | 14 | 1.4758562462 | 0.0931123517464 | 0.650390174866 | 1.33687388836 | -0.0435335344022 | 2.66728404906 | -0.0380925344843 | -0.00644553654553 | -0.1161928447 | -0.0774733226581 | 0.154753965875 | 0.208562837134 | -0.0576924442968 | -0.22053616732 | -0.118636247556 | 0.173140863136 | -0.0246306616554 | 0.00131071295071 | 0.250993847252 | 0.0123473882485 | 0.269837875846 | -45.4986052291 | -10.829998601 | 31.7669261375 | 15 | 8.60028267785 | 1.93314476772 | 4.66792706525 | 3.57985900601 | 3.29114397266 | 9.35722233696 | 0.0107349845031 | -1.07019560184 | -0.00426366101675 | 1.49508031292 | -0.281779967764 | 0.982351799586 | -0.106659674768 | -0.763349553134 | 0.192179880365 | 0.750978420031 | 0.111024994292 | 0.184811442899 | 0.612900702521 | -0.00365657178532 | 0.459549042635 | -45.2324744703 | 1.54403828843 | 53.5789452489 | 16 | 6.33490374753 | -0.485857405263 | -0.907753889929 | 3.37707099471 | 4.10812050677 | 5.00448286801 | 0.103659840782 | -1.21233768852 | 0.819700587374 | 0.898260415924 | -0.320237478177 | 0.290566367226 | -1.30233851021 | -0.0797941991629 | -0.0482422653662 | 0.964985055607 | 0.0699073893153 | 0.041299279641 | 0.548754046083 | -0.135226699587 | 0.380063038565 | -39.9747788941 | 8.39265222464 | 53.7283345794 | 17 | 2.14611125224 | 0.0302658665538 | 0.787049721871 | 1.83269262153 | -0.0136332123832 | 1.79897501926 | -0.110249121666 | 0.0324029040821 | 0.0302814819527 | 0.0289099065673 | 0.13055706502 | 0.135197350414 | -0.207166324814 | -0.104552473655 | -0.0297731165431 | 0.261984674213 | -0.0337916198227 | 0.0235240989495 | 0.218904969437 | 0.0205599870206 | 0.206722564047 | -40.4324877366 | 2.85548835818 | 30.8431911908 | 18 | 0.391480441523 | -0.770285754102 | -0.868672928614 | 3.11060769427 | -0.0168394778412 | 4.88908753008 | 0.0529173434785 | 0.0162290889147 | -0.51956312557 | -0.207396747744 | 0.0386680964263 | -0.197122561435 | 0.327458520067 | 0.0588014505203 | -0.0857667350787 | 0.231034689411 | 0.0196431749535 | -0.0397532166819 | 0.179009356535 | -0.0181396260435 | 0.510481743132 | -23.5543842836 | -35.6878726552 | 43.6313725778 | 19 | 5.78193160974 | -1.17109327312 | 0.271416438997 | 3.26490295396 | -0.255236217525 | 2.00006264307 | 0.0135115022432 | 0.049388022008 | -0.885364436861 | -0.154224923178 | 0.015280637132 | -0.0585801675377 | 0.380430924445 | 0.0494742058448 | -0.0213335217225 | 0.285602971722 | -0.0279074767362 | -0.0340856112887 | 0.230598923373 | 0.0151019207019 | 0.536926780373 | -26.5714133447 | -40.0162555796 | 45.6520572737 | 20 | 2.03079890852 | -1.89979949209 | 1.74926631329 | 3.75982612684 | 0.163197617285 | 4.2857165008 | -0.161859434544 | -0.765685446751 | -0.650036805328 | 0.394662264637 | 0.215104021799 | 0.249921757248 | 0.00794774421469 | -0.4551736043 | -0.0898524273732 | 0.273211167556 | -0.0461372496607 | 0.00788189627433 | 0.368339554039 | 0.112752969084 | 0.465514578101 | -34.1574003927 | -34.0354451373 | 54.4093517902 | 21 | 1.20641639401 | -0.00023202765917 | 0.779375794379 | 0.943312376764 | -0.252063534811 | 1.67461670352 | 0.0522395393267 | -0.019019933255 | -0.27687941312 | -0.0429079763478 | 0.0913476092851 | 0.0211856414297 | 0.133705970843 | -0.0592549296448 | -0.156642656693 | 0.18624840879 | -0.0280299060724 | -0.00483446465281 | 0.207661478909 | -0.0142717260306 | 0.304154116388 | -33.3987394758 | -22.3609850437 | 39.7342014956 | 22 | 8.69488708597 | 1.42291779732 | 4.50900491929 | 6.14854822249 | 2.38504916104 | 4.04595281295 | -0.0839609858249 | 0.604903391708 | -1.14478977587 | -0.56218734539 | 0.305966617674 | 0.451891430005 | 0.822230358243 | -0.640158752251 | -0.158228601231 | 0.652902971613 | -0.134692251254 | -0.0347295765785 | 0.5005973291 | -0.196062475493 | 0.701853196405 | -34.5705507142 | -34.4082202499 | 19.2362961551 | 23 | 1.00935303471 | 0.942470379832 | 1.98462125724 | 7.91082291102 | 5.45318228839 | 5.79295475254 | -0.196380288159 | 0.973602107043 | -0.782285980732 | -0.605149340497 | 0.444369303408 | -0.641235770209 | 1.37182860536 | 0.424607022186 | -0.42137907208 | 0.801484638227 | -0.0552199834896 | 0.0199670327665 | 0.699200476797 | -0.30555346197 | 0.589345484894 | -28.422080762 | -32.4854895581 | 13.407682914 | 24 | 1.41558507666 | -0.376544480088 | -0.00940564611877 | 1.51012058863 | -0.095715876941 | 3.22780702249 | 0.0232894021366 | 0.211735198793 | -0.270865248515 | -0.143876831014 | 0.0459590104285 | -0.14690454087 | 0.139939045263 | 0.236419045789 | -0.085065581987 | 0.180702864512 | -0.031446071918 | 0.0230872772003 | 0.250594073973 | -0.0715557852215 | 0.337843692342 | -20.6100338165 | -21.284181758 | 32.6024977224 | 25 | 3.99742202214 | 2.0996758017 | -0.246730843082 | 2.00233239376 | -0.651120525189 | 2.24750920891 | -0.0175169026583 | -0.0402574700018 | -0.163065222076 | 0.163096547502 | -0.152584713241 | -0.752605848676 | -0.114263147423 | 0.55594900455 | 0.0505230130035 | 0.217813308706 | -0.0577874222086 | -0.0155529046226 | 0.556670648365 | -0.0038561932793 | 0.548348630501 | 2.46808642882 | -11.2128787153 | 36.6681388133 | 26 | 4.21305278142 | -0.5601098332 | 1.51243635319 | 4.07377310611 | -1.51196754142 | 2.41865819014 | -0.00170095898662 | 0.0871065546514 | -0.266401338515 | 0.1052309084 | -0.154446189383 | -0.729264935342 | -0.181283540011 | 0.872204081406 | 0.15713791959 | 0.253813792718 | -0.115442506091 | 0.00594378446983 | 0.698911706493 | -0.0170785026799 | 0.638031367326 | 7.65730288611 | -9.23127533789 | 36.1907593836 | 27 | 3.09352352612 | -2.68220308742 | 0.255843959533 | 6.17311463515 | -0.211635229207 | 1.39861709604 | 0.0499309814821 | 0.830806877447 | -0.337368660081 | -0.757962860642 | -0.299920464908 | -0.692697322503 | -0.11823722638 | 0.557898050388 | 0.252639354982 | 0.322295426281 | -0.17182343308 | 0.148733266299 | 0.953965655262 | -0.0495038223803 | 0.627714252564 | 7.24839768594 | -7.5217665501 | 22.9118388917 | 28 | 1.00027533589 | -0.0575182629262 | 0.190116848942 | 1.32678264136 | 0.0243195721521 | 1.25359718408 | -0.0662221726476 | 0.207347387987 | -0.0452953595171 | -0.0942434886299 | 0.0194248984731 | -0.375935954787 | -0.171566140716 | 0.403778602202 | 0.0437219450576 | 0.213069107731 | -0.114210863179 | 0.0395728996965 | 0.393572107569 | -0.0273403280251 | 0.305913008345 | -10.2929751983 | -3.99205980813 | 28.3932482058 | 29 | 8.14812962382 | -6.69715656454 | -6.29970524698 | 6.07873744921 | 5.2186912181 | 5.59446695784 | -0.182344786315 | -0.00274729629351 | 1.00724602858 | -0.000584694575799 | 0.493289311414 | -1.13864362142 | -1.22006965637 | 0.804077514859 | -0.299567780379 | 0.59743270927 | -0.149493512862 | -0.159411323482 | 0.422541776804 | -0.0144370699529 | 0.483112875124 | -10.3907564214 | 9.0333148742 | 48.2645746353 | 30 | 8.51121496865 | 1.3219431039 | -1.40058827856 | 1.01100818931 | 2.10023294114 | 6.95763026046 | 0.384318392408 | -0.618630568799 | 0.0696815406702 | 1.20155986521 | 0.119166062245 | -0.548265774169 | 0.513835565981 | 0.2076120196 | -0.344983428105 | 0.730389264598 | -0.0622502927122 | -0.157884333981 | 0.353936496073 | -0.0168748450344 | 0.344840749516 | -15.5238717207 | 6.13420120801 | 54.5323403798 | 31 | 1.87014427031 | -0.244313637385 | 0.06765532265 | 1.45133098274 | 0.293475648184 | 2.43416417275 | -0.0819060699465 | 0.0607310353627 | -0.208481247319 | 0.0820943961864 | 0.0600202826408 | -0.209276408147 | -0.0373128040772 | 0.270898611024 | 0.008105670481 | 0.217574711275 | -0.0631147482445 | -0.00660865541266 | 0.290428327746 | -0.0234736156496 | 0.322866317481 | -15.8450250434 | -11.8017666756 | 39.5517072145 |
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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 |
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1 | 1 | chain 'A' and (resid 5 through 47 )AA5 - 47 | 1 - 43 | 2 | 2 | chain 'A' and (resid 48 through 71 )AA48 - 71 | 44 - 67 | 3 | 3 | chain 'A' and (resid 72 through 85 )AA72 - 85 | 68 - 81 | 4 | 4 | chain 'A' and (resid 86 through 108 )AA86 - 108 | 82 - 104 | 5 | 5 | chain 'A' and (resid 109 through 137 )AA109 - 137 | 105 - 133 | 6 | 6 | chain 'A' and (resid 138 through 195 )AA138 - 195 | 134 - 191 | 7 | 7 | chain 'A' and (resid 196 through 209 )AA196 - 209 | 192 - 205 | 8 | 8 | chain 'A' and (resid 210 through 223 )AA210 - 223 | 206 - 219 | 9 | 9 | chain 'A' and (resid 224 through 266 )AA224 - 266 | 220 - 262 | 10 | 10 | chain 'B' and (resid 5 through 47 )BB5 - 47 | 1 - 43 | 11 | 11 | chain 'B' and (resid 48 through 71 )BB48 - 71 | 44 - 67 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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