Software | Name | Version | Classification |
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PHENIX | 1.20.1_4487refinementAimless | | data scalingautoPROC | | data processingSTARANISO | | data scalingXDS | | data reductionPHASER | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→61.87 Å / SU ML: 0.2489 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0256 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2466 | 3856 | 5.02 % |
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Rwork | 0.199 | 72990 | - |
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obs | 0.2014 | 76846 | 50.69 % |
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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: 18.36 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.85→61.87 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 14816 | 0 | 72 | 1128 | 16016 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0035 | 15422 | X-RAY DIFFRACTION | f_angle_d0.6115 | 20885 | X-RAY DIFFRACTION | f_chiral_restr0.0458 | 2230 | X-RAY DIFFRACTION | f_plane_restr0.0048 | 2726 | X-RAY DIFFRACTION | f_dihedral_angle_d12.7083 | 5791 | | | | | |
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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 | 0.254646757465 | -0.168765294701 | -0.115355703129 | 0.30812096546 | -0.0979039491967 | 0.222320118055 | -0.00657448926952 | -0.05683205261 | 0.144175908293 | 0.182752718088 | 0.0201537420143 | -0.0916004894433 | -0.0794657288337 | 0.0610801964995 | 0.0342390243865 | 0.0590967416511 | -0.0838329633507 | 0.0237470303518 | 0.00714679605467 | -0.0439996985211 | 0.0382206574497 | 11.5569240302 | 24.440531192 | 29.0399102547 | 2 | 0.727774038101 | 0.157715044652 | -0.0845896845674 | 1.0792489913 | -0.242198638171 | 0.211561941736 | 0.0446399846748 | 0.0843436689083 | 0.158023441585 | -0.0208216797419 | 0.00868678752485 | -0.0816768650547 | -0.130513269604 | -0.0304434653741 | -0.0160334459137 | 0.162277480027 | 0.000683121569114 | 0.0506391147734 | 0.0398185841546 | 0.0516657355908 | 0.170682741955 | 11.4853330404 | 45.5368193448 | 15.1666820172 | 3 | 0.257092620714 | 0.0224300329813 | -0.081599577657 | 0.217595933544 | -0.0648834282545 | 0.325791999041 | 0.0275178540093 | 0.0876901611689 | 0.191193433701 | 0.0702649758367 | -0.0249159977365 | 0.12142752491 | -0.192448297711 | -0.151490691451 | 0.0539991170516 | 0.0378230406988 | 0.0484267154054 | 0.0399730167757 | 0.0390050626321 | 0.0346843051421 | 0.127801998648 | 3.23796953368 | 35.6863633663 | 17.7200567905 | 4 | 0.942074839014 | 0.0179211139954 | 0.611284951204 | 0.57375140663 | 0.075998884396 | 0.483107978271 | -0.0589473321207 | 0.0401749257961 | 0.388800636899 | -0.011546614826 | 0.0318404960783 | -0.255900697084 | -0.311768127306 | 0.110503331586 | 0.0497417991254 | 0.305659797395 | -0.043845521564 | 0.0684720600893 | 0.0603997466848 | -0.0361270952167 | 0.243767893636 | 14.5711450755 | 44.7918192707 | 35.6915514815 | 5 | 0.738071281172 | -0.307701457983 | -0.15564226848 | 0.256276489514 | -0.190125285847 | 0.54288482692 | 0.0269581823195 | -0.229703913217 | 0.38948893772 | 0.131653978742 | 0.00434951470702 | -0.254885810368 | -0.423304286554 | 0.275106633571 | -0.100543838979 | 0.407285642395 | -0.0933267703204 | 0.0619040912779 | 0.187409493705 | -0.0846917481099 | 0.308011392664 | 20.7092518849 | 42.7855198161 | 40.5795460336 | 6 | 0.239052746362 | -0.0532831346874 | 0.0954796299767 | 0.303936304329 | -0.00309807275114 | 0.125074346285 | -0.000472972894598 | 0.112573654922 | 0.00383969854192 | -0.0293577634084 | -0.0868756393049 | -0.00297149445957 | 0.00479642427844 | -0.020257609072 | -0.105242827159 | 0.0670321813129 | -0.0267511091386 | -0.0567569127246 | 0.0754075075855 | -0.0408678296982 | 0.0453673912273 | 21.8076271998 | 10.0897424183 | 16.3279982128 | 7 | 1.05968658811 | 0.0426535016425 | -0.651554741346 | 0.00963614063175 | -0.0999379741974 | 1.08297704612 | 0.016242206977 | -0.0346581418445 | 0.256739262736 | 0.000629545394754 | -0.0405866899499 | -0.0326615902746 | -0.119925874882 | 0.195123655012 | -0.0581368578713 | 0.0555676263681 | -0.00741552412553 | 0.0242971138078 | 0.118839003606 | 0.0968745260318 | 0.251299419532 | 38.5736759546 | 31.4477316921 | 9.34295027119 | 8 | 2.0923703791 | -0.6830396156 | -0.538612613806 | 0.697356225998 | 0.327821814622 | 0.529766332863 | 0.0480864241052 | 0.211956481389 | -0.0296212530292 | -0.0853219790658 | -0.118643634627 | -0.0555182650962 | 0.0102299848992 | -0.016327257349 | 0.0713740491404 | 0.0694395844068 | 0.0383703798558 | 0.0555128425771 | 0.20517060551 | 0.102057661388 | 0.200624688718 | 38.1113289085 | 23.1857087361 | 1.26707543694 | 9 | 0.242099432186 | 0.0138886430223 | 0.0471888508653 | 0.0386921272172 | 0.0637043425222 | 0.109320451006 | 0.0292873234162 | 0.028521675344 | 0.0672237468734 | -0.00113327316523 | 0.0246232972492 | -0.226805745278 | -0.035993502281 | 0.104991891286 | 0.0767272273438 | -0.0697010895004 | -0.0617181665944 | -0.00846302758131 | 0.0794185855159 | 0.0435455077786 | 0.306035530975 | 42.8667404542 | 17.7885203677 | 13.2340108865 | 10 | 0.333813783156 | 0.0614624807383 | 0.0629011330319 | 0.169344122951 | 0.116878087453 | 0.176387482978 | 0.01097052397 | -0.00643860408406 | -0.0612492225006 | 0.00315964942602 | 0.00775894815928 | -0.0752026570144 | 0.00917590074537 | 0.0316240447662 | -0.0342162041726 | 0.010312534463 | -0.0267650208819 | -0.0221155603875 | 0.0240011564286 | 0.0180797506192 | 0.0825682962247 | 29.6638656288 | 7.13201035452 | 17.3555178077 | 11 | 0.603088378094 | -0.00223684705675 | -0.353271610273 | 0.222113795829 | 0.174539310702 | 0.341927940267 | 0.15554362732 | 0.298520805137 | 0.203776999264 | -0.235822140798 | -0.0639660013776 | -0.080057276255 | -0.203104159631 | -0.13363562285 | -0.142665854613 | 0.226294974135 | 0.0616444887318 | 0.15547393117 | 0.167644988446 | 0.0279458596976 | 0.168923313577 | 32.6455521168 | 5.96729950864 | -7.02721574399 | 12 | 0.668542349 | 0.463732632919 | 0.195580791664 | 1.05602032257 | -0.233243225598 | 1.536707361 | -0.00777529301038 | 0.325711539427 | 0.273733559141 | -0.311121488593 | 0.00322243469618 | -0.145805737571 | -0.219055387913 | 0.0874065902997 | -0.0311089742723 | 0.153643700123 | 0.0419053389282 | 0.091615872535 | 0.160226317091 | 0.0686956776697 | 0.189558776691 | 26.7299182828 | 11.263937548 | -2.88481628657 | 13 | 0.53999488636 | -0.0944763470606 | -0.095437693198 | 1.33546641246 | 0.288136442611 | 0.072553014206 | 0.109394104882 | 0.379012807697 | 0.0571645250308 | -0.561183603441 | -0.100026682567 | -0.0666914724059 | -0.149339257112 | -0.109207757273 | -0.0975244333618 | 0.299264058955 | 0.0471411583952 | 0.102336602166 | 0.247770255317 | -0.0121457929625 | 0.145545981525 | 21.3395975802 | 8.58869813096 | -7.17892921307 | 14 | 0.302503454451 | 0.00311053147119 | -0.0785955997105 | 0.564961555729 | -0.0324509405697 | 0.578939740361 | 0.0569758017193 | -0.0429970729488 | 0.0428836454231 | 0.000395143317108 | -0.00603969312426 | 0.0984805475783 | 0.0143461059617 | -0.104536091538 | 0.0218481724076 | 0.0941346644728 | -0.0486667892649 | -0.0267951071784 | 0.0452765384281 | -0.0228689848761 | 0.0327859608697 | 2.94622539546 | 6.20859491918 | 42.738049564 | 15 | 1.38778747434 | 0.326101600593 | -0.364071661978 | 0.302169980903 | -0.724560546292 | 1.90762774185 | -0.0483737199474 | -0.306944419977 | -0.258710948991 | -0.0640289809378 | 0.0293130769001 | -0.00681020493913 | 0.406187998825 | 0.0857664732531 | 0.0539212603531 | 0.317693479041 | -0.0328568608731 | 0.0852847226407 | 0.16248447043 | 0.0478633791412 | 0.113556854512 | 1.87965861132 | -15.4907550074 | 60.7985903477 | 16 | 0.122672039966 | -0.0268918532456 | 0.0517623039469 | 0.156788544352 | -0.154560258257 | 0.495878906776 | 0.0204518966678 | -0.0818752760514 | -0.0423797023079 | 0.0315395534434 | 0.0364060307347 | 0.0272216729001 | 0.114703154591 | -0.101172458647 | 0.0688153270232 | 0.335502582884 | -0.0644899626912 | 0.072000509233 | 0.236157852439 | 0.0248275980659 | 0.0490306708239 | -2.91955062754 | -4.50120508731 | 68.2879023013 | 17 | 0.130503123883 | -0.00921119346137 | -0.0358914113928 | 0.102265261212 | 0.0109006333627 | 0.22250022874 | 0.0328505854377 | -0.134143563866 | -0.0120890674418 | 0.216342563882 | -0.00037120113011 | -0.0485065611229 | 0.052872860659 | 0.0786791246393 | -0.056526435404 | 0.258858876802 | -0.0652745922718 | -0.0375025779996 | 0.107067725993 | -0.0147192959321 | -0.0218792185517 | 8.95087583112 | 1.74956406308 | 57.3695349958 | 18 | 0.251107168101 | -0.141589526721 | 0.218283460651 | 0.148293776473 | 0.00508248894906 | 0.438021130535 | -0.0479792732416 | -0.115866781444 | -0.11247667673 | 0.173068177512 | 0.00479419439236 | 0.163963812708 | 0.185742839888 | -0.19668297782 | 0.17623419881 | 0.286429205021 | -0.00322719494401 | 0.148209867206 | 0.104868815058 | -0.0217996745671 | 0.0886727442204 | -13.4845090621 | 9.0075786787 | 55.1573455095 | 19 | 0.726411775018 | 0.881198335831 | 0.619065961779 | 3.88744253697 | 1.98572208797 | 1.43297847372 | -0.0295123133822 | -0.176101192982 | 0.161744641794 | 0.0371827597269 | -0.0309826453138 | 0.67075231551 | -0.12728463814 | -0.454121790779 | 0.0944504121166 | 0.315678468546 | 0.0134239291756 | 0.169485847016 | 0.304344694646 | 0.0367071734377 | 0.331575046641 | -22.9003074468 | 1.91317864456 | 50.4027640214 | 20 | 0.446798130602 | 0.193751901705 | -0.199078752232 | 0.441113299386 | 0.225892604712 | 0.537197530116 | 0.00957576259565 | -0.0593191563123 | -0.0355463855681 | 0.113827851632 | 0.0379392933689 | -0.114820682051 | 0.15969612963 | 0.0653323739428 | -0.0529040297549 | 0.0774842264132 | -0.0470340178214 | -0.0336026100107 | 0.0279890610126 | -0.00575595309842 | 0.0652760688957 | 11.6020375049 | -8.39630912332 | 28.8282266117 | 21 | 0.429079832714 | -0.485084866182 | 0.460583039301 | 1.76920361961 | -0.000566388637615 | 0.716297584191 | -0.0342918178764 | -0.035121522356 | -0.087003459116 | 0.153402203593 | 0.0316041838502 | 0.16392150846 | 0.0849541221495 | -0.179134551866 | -0.0176299211229 | 0.235156557068 | -0.0657684325118 | 0.0300637489846 | 0.0833779337917 | -0.00235825182401 | 0.0659727779075 | -7.66871409001 | -26.2213429844 | 39.0698584516 | 22 | 0.204238993644 | 0.164837937097 | -0.0798254460115 | 0.256444756041 | -0.126748856484 | 0.127509921862 | 0.0309523925264 | -0.0518219396082 | -0.0504597401482 | 0.0988688577821 | -0.0397665268321 | -0.0122456990983 | 0.0599007256371 | -0.0401119819779 | 0.04194034196 | 0.281384639906 | -0.101545617519 | 0.0586868477383 | 0.054227951821 | -0.00873094650408 | 0.0960876113889 | -0.999290748455 | -33.6616610944 | 28.7893477584 | 23 | -0.00187091654705 | 0.00561035284733 | 0.003801062644 | 0.088306486141 | 0.138922053539 | 0.232327076393 | -0.0317376959383 | 0.0751213345788 | -0.0816343044066 | -0.0160985222906 | 0.0505414211871 | -0.0322207644181 | 0.148354169737 | -0.080898678035 | 0.133880166038 | 0.129755229102 | -0.136951947313 | 0.00913446952999 | -0.0210133318667 | -0.136500450653 | -0.000315537877127 | -1.02418642173 | -17.1449403352 | 23.5353169852 | 24 | 1.46716874513 | -0.143984510915 | 0.667918856946 | 0.0967140192533 | -0.149517662422 | 0.386834007431 | 0.0205058685154 | -0.24040511342 | -0.496073647498 | 0.439102840658 | 0.0813977104349 | 0.0177819180872 | 0.394107196174 | -0.0694839776271 | -0.0169809245691 | 0.459999536019 | -0.00587142054105 | 0.0647217699337 | 0.0970960835573 | 0.00435842128223 | 0.253302715006 | 18.3899597888 | -28.8269744754 | 29.3735771831 | 25 | 1.04741298972 | 0.413471596086 | -0.564817625357 | 1.12743224097 | -0.210488615029 | 2.25263987305 | -0.0741838282602 | -0.314102612647 | -0.463222321461 | 0.406936224697 | 0.0300489302897 | -0.238293137655 | 0.627572714208 | 0.447978636286 | 0.100236842606 | 0.454299187517 | 0.105078009384 | 0.022987895678 | 0.24614492716 | 0.0270389216261 | 0.361871848267 | 25.4336080461 | -26.9930900761 | 33.0724273649 |
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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 2 through 99 )AA2 - 99 | 1 - 98 | 2 | 2 | chain 'A' and (resid 100 through 168 )AA100 - 168 | 99 - 167 | 3 | 3 | chain 'A' and (resid 169 through 341 )AA169 - 341 | 168 - 340 | 4 | 4 | chain 'A' and (resid 342 through 423 )AA342 - 423 | 341 - 422 | 5 | 5 | chain 'A' and (resid 424 through 467 )AA424 - 467 | 423 - 466 | 6 | 6 | chain 'B' and (resid 2 through 99 )BE2 - 99 | 1 - 98 | 7 | 7 | chain 'B' and (resid 100 through 132 )BE100 - 132 | 99 - 131 | 8 | 8 | chain 'B' and (resid 133 through 155 )BE133 - 155 | 132 - 154 | 9 | 9 | chain 'B' and (resid 156 through 295 )BE156 - 295 | 155 - 294 | 10 | 10 | chain 'B' and (resid 296 through 342 )BE296 - 342 | 295 - 341 | 11 | 11 | chain 'B' and (resid 343 through 371 )BE343 - 371 | 342 - 370 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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