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- EMDB-46661: Mycobacteriophage Bxb1 tail tip - Composite map and model -

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Basic information

Entry
Database: EMDB / ID: EMD-46661
TitleMycobacteriophage Bxb1 tail tip - Composite map and model
Map dataMycobacteriophage Bxb1 tail tip - Composite map and model
Sample
  • Virus: Mycobacterium phage Bxb1 (virus)
    • Protein or peptide: Major tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Tapemeasure protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
KeywordsBacteriophage / tail tip / VIRAL PROTEIN
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Fibronectin type III / Beta-lactamase/transpeptidase-like / Immunoglobulin-like fold
Similarity search - Domain/homology
Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Tapemeasure protein / Major tail protein / Minor tail protein
Similarity search - Component
Biological speciesMycobacterium phage Bxb1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsFreeman KG / White SJ / Huet A / Conway JF
Funding support United States, Taiwan, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI173544 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116884 United States
Howard Hughes Medical Institute (HHMI)GT12053 United States
National Institutes of Health/Office of the DirectorS10 OD025009 United States
National Institutes of Health/Office of the DirectorS10 OD019995 United States
National Institutes of Health/Office of the DirectorS10OD032467 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
Academia Sinica (Taiwan)AS-IDR-110-06 Taiwan
CitationJournal: To Be Published
Title: Structure and infection dynamics of mycobacteriophage Bxb1
Authors: Freeman KG / Mondal S / Macale LS / Podgorski J / White SJ / Silva B / Ortiz V / Huet A / Narsico JT / Ho MC / Jacobs-Sera D / Lowary TL / Conway JF / Park D / Hatfull GF
History
DepositionAug 20, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46661.png

Downloads & links

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Map

FileDownload / File: emd_46661.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacteriophage Bxb1 tail tip - Composite map and model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0035228988 - 2.0512252
Average (Standard dev.)0.0019892624 (±0.029947754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 513.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mycobacterium phage Bxb1

EntireName: Mycobacterium phage Bxb1 (virus)
Components
  • Virus: Mycobacterium phage Bxb1 (virus)
    • Protein or peptide: Major tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Tapemeasure protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Minor tail protein

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Supramolecule #1: Mycobacterium phage Bxb1

SupramoleculeName: Mycobacterium phage Bxb1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Tail tip complex of Bxb1, containing ten protein subunit types. This is a composite map, and related entries for consensus and locally refined maps are noted.
NCBI-ID: 2902907 / Sci species name: Mycobacterium phage Bxb1 / Sci species strain: Mycobacterium phage Bxb1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Virus shellShell ID: 1 / Name: Mycobacteriophage Bxb1

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Macromolecule #1: Major tail protein

MacromoleculeName: Major tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 30.170271 KDa
SequenceString: MALKDDAVLI AARGYVYTAA VGTAAPTPSQ LKLIDLEHPE AWDRTGWDLV GHTSEDDLPE FGFDGGDSEV RGSWQKKKLR EVETEEIAD YVVINLTQFD ETALELYFGP NQSATPGIFG VKSGSVVNER ALLIVIVDND VRLGFHARKA SLKREDAISL A TDEFGALP ...String:
MALKDDAVLI AARGYVYTAA VGTAAPTPSQ LKLIDLEHPE AWDRTGWDLV GHTSEDDLPE FGFDGGDSEV RGSWQKKKLR EVETEEIAD YVVINLTQFD ETALELYFGP NQSATPGIFG VKSGSVVNER ALLIVIVDND VRLGFHARKA SLKREDAISL A TDEFGALP VRATFLDYQS YNLYEWIEED WFNAVDAPVV YLLDLGGATG GDYTLLVGGK STGDIAYNAN ASAIKTAIGA VD DGVAESA WTVTADGSDF EISGPLAVAL GVDSTTGGSG VTVDVV

UniProtKB: Major tail protein

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Macromolecule #2: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 9.696724 KDa
SequenceString:
MTTVTATVHD ISGRPDDSHW TFSSDLREQD GVIITPRVVR VKPFNGELAL TLPPGPVRVT HHQDRWLIDV PEEDSDLWDL IEAATD

UniProtKB: Minor tail protein

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Macromolecule #3: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 36.723973 KDa
SequenceString: MTVTITADVR DVTGQPDNQQ WVFSTVLRQQ DGSILTQKQV RVNPVDGALS VELEPGFAIV VYGEYRWFIE VPETDAGLWG LIATSVAVP PDTSAELLAD AVNGYLDANP PSADWDALSN VPSEFPPSAH DHVAADVTDL DSAIAAYLAS NPPEAGSVAW D DIDDKPST ...String:
MTVTITADVR DVTGQPDNQQ WVFSTVLRQQ DGSILTQKQV RVNPVDGALS VELEPGFAIV VYGEYRWFIE VPETDAGLWG LIATSVAVP PDTSAELLAD AVNGYLDANP PSADWDALSN VPSEFPPSAH DHVAADVTDL DSAIAAYLAS NPPEAGSVAW D DIDDKPST FTPSSHTHSI ANVTGLQDAL DEKLDEAAVD ARVSLGTAAL VDSAPSTLDT LNELAAALGD DPNFATTVAS QI GAKADKA TTITAGTGLT GGGDLSANRT LNVSFGTSST TACVGNDSRL SNTRTPTDGS VTNAKVASGA GIALSKLATG YVA GSDNSG ARTLTIWVGT EAQYTAIGTK DSNTIYLRTA

UniProtKB: Minor tail protein

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Macromolecule #4: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 74.357398 KDa
SequenceString: MASRLLDPDT LVELEGVNGE WFDLTNGTEG IYLATEVTGL LDPPVKATYE EPGNFPGARY LNHRVLRRDL VFGVEILNDE NDETWLRRD SAWRKAWSFK RDAKLHITTG ESGHRYLKVR LFESPTTDMV TDPRGREVNI TKMVVVAGDP FWYEDDVVYP I EVQEDTTF ...String:
MASRLLDPDT LVELEGVNGE WFDLTNGTEG IYLATEVTGL LDPPVKATYE EPGNFPGARY LNHRVLRRDL VFGVEILNDE NDETWLRRD SAWRKAWSFK RDAKLHITTG ESGHRYLKVR LFESPTTDMV TDPRGREVNI TKMVVVAGDP FWYEDDVVYP I EVQEDTTF DPNPLPWPWP QPELPVEDIE ITVPNANPTD NIIWPKWTLP GSSEKPAEPY IPGLPWLGAP KSPATLWTVP DY KLDLDED EDPSLGTRRI RMPGQIGGLR VEEVQQIYID GRPTGGTFKI GYGDEWTEPI AYNASPNDVR AALIALEGIS AND VEVSLG GATNEVQTVR LKGGALGGTF TLSLGSETTV GIPFNASDAD LQGALVGLDS IGSADVRVKS TKINEVQVVE LVGE PTSGS FTLTLDGQTT APIAYNATPA TVAARIADLP NIDGNYVKVE GLNEWFHSPY RITFGEAQSQ GVITDIISGI IDFIG GLFG GNASGKGVGG IDIDEMTGDV GTLSGGAGLD VQVTTEQDGD RLYVVSFQRA AGGLNLPQLV GNASGLEGDD LSIETA TNV DGGRPYVVRF TDDLQGVDVP TMTVDTDDLT GGYEVGSRVV VLREGYTYPA ENVVVDSDPR EEQVSSESGS PIWERMN SV RFLHYIPPYT GEVTFKLSVS GAVPGQIATL RLPRAWSRPW GLE

UniProtKB: Minor tail protein

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Macromolecule #5: Tapemeasure protein

MacromoleculeName: Tapemeasure protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 84.842367 KDa
SequenceString: MAAGKEVGRL SIKVTPDLDG FYRELKAAVE AAEKMKVHIP VEPDMGNFRQ EVAASTAGMS TRVKVQADVD RGLLDRLSNS LSGMKAPSF GSGINPTGYM LILGAAAALT PLIAGSLGAI SAALLTLPGL IAAVAVPIGA LALGIDGFKR AAERLKPAFD G LKESMSAA ...String:
MAAGKEVGRL SIKVTPDLDG FYRELKAAVE AAEKMKVHIP VEPDMGNFRQ EVAASTAGMS TRVKVQADVD RGLLDRLSNS LSGMKAPSF GSGINPTGYM LILGAAAALT PLIAGSLGAI SAALLTLPGL IAAVAVPIGA LALGIDGFKR AAERLKPAFD G LKESMSAA VENQFGPVFD QLGKAIPTLA ANLPKVTQGM ADVAKSIVDS VTSGEGLGRI ESLISNIGAA ISRSAPGLTS FV DGLLNLA EKFSGKLPAI ADWINRTGES FSKWVTDFTT AGPDGVSKFD NAMSGLGDTL QMLGGGLVDI LNKSLEFFSD PQK IQSFKA ELDGLIASIS TLVDLINSLA AAFSKVPGLS DGEANGVMDF APIQIQGAIE LIKQIPTAWE GVKLKAAEVW NSIP TMAAT AIASIRATLA TLPGLLSGIW TTVTASASSA FATIGAAVSA GARSVVNTAG NIFRSMGSVI ANAFSAAVSA VQTAF SQMV SAAASGAQQV VAEVQALGGK IAAAAGNFGS ILVAAGKALM DGLLSGIKAG LSAVLDFASG IAAKIAAVKG PLPKDR KEL IPAGEALMEG LGTGIENGLD PVLDRAREIA KQIFSAFKET FGTAPTSLAF NLGSMQGDLS GLQTSLESTA TASRDLT SS LTAPTAELAS GSSLLGDDVK DQLDELKLAY DQLELQRKQL KVQKNEAGSK EDKAAIQDKI DALQAEKDKL AYQKDQLK I QQKQTGEMGE QKTLAQFLGE QIASTWQQGT DAVAGFARSN LDQAMSDLGI GGGAITNGLN AGLDWGVQAL GNAVNIQVN SVDDAIAVKN NEVNKQALTY TRR

UniProtKB: Tapemeasure protein

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Macromolecule #6: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 67.065172 KDa
SequenceString: MPAPAADMTT LAGHQQLWDT VMKRRQKRED ERIAPPLIRL WDGDYKLRGQ LVGERSHKFE FIENETGTAS ITISLDHYLA KWIASHKGR ARRNVHVSFD KQGARWTGRM DHYDIVRTKE GDVYMEVVFK HDYEELKHIY VWANPFLRPE FQFPKLWVMF G PAKWALLL ...String:
MPAPAADMTT LAGHQQLWDT VMKRRQKRED ERIAPPLIRL WDGDYKLRGQ LVGERSHKFE FIENETGTAS ITISLDHYLA KWIASHKGR ARRNVHVSFD KQGARWTGRM DHYDIVRTKE GDVYMEVVFK HDYEELKHIY VWANPFLRPE FQFPKLWVMF G PAKWALLL TLFVNILRLE TSLWTLPDNP LDISEWFPFS LNPGNWRNIV KPFPFLADNS PLTIVFSRFK SFHDTAKNVL AD SQLTIVC RRYFHGEDPH PFAELSGELG LPLIEGIASL IPLRHGCLVW DIVDNSGWGS ETAFGGSLLT GLVRAVMNIA SDG MTEGID IYTGLPTYPG EYYTPGFLGT YPKAPHVVFM ESPYTGIESS KFTYTEATDT SFVLGGQSMP GVNEVISAGI NMGG DFLTS LINSQLATLG AFGGAIDLPP LGGIMDAVAR PLYENVVLAF MEIPTLRAAG LSLPIAGLED IVTGLGDFHY NEGWV DGAD KAFTISAIMA ARAKQWATRA KHSHEIQVSD AAPYIIGERG HGHFWLGDRV GTTVLGYPDP YTIFVERVTK LTYEWT SDG PKGWTITIGY KEPEDPILKA FELIQYINSN LGQLGIL

UniProtKB: Minor tail protein

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Macromolecule #7: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 64.05623 KDa
SequenceString: MADDQWVPDV PDGAFVIGGG DYRYGQDMTE DIARSLFQVP DFNPANALLV LPQLLLRLPL EALQKFKDFI PNVLEGAFNT VAGAVDAIM GAIRETPRVL EQILSYLPQE LRDELEHAAA RIGAVIDAIV QALTGTLNIG HTIEDLIFSL TNIRPGAVGG V LGGGSIEE ...String:
MADDQWVPDV PDGAFVIGGG DYRYGQDMTE DIARSLFQVP DFNPANALLV LPQLLLRLPL EALQKFKDFI PNVLEGAFNT VAGAVDAIM GAIRETPRVL EQILSYLPQE LRDELEHAAA RIGAVIDAIV QALTGTLNIG HTIEDLIFSL TNIRPGAVGG V LGGGSIEE TIKRIVDAIV SGIVGVTGIG AGISDLQSLI EQISSAAARG GFAWDILGIQ NNKKPKSGLY KSERGNFDLD TL NSTVSVA PGTSIIAFDV IEQSMPIGLI TWIGWGTSGI TEFYINVYRC VDDRSDPELG ELIHQSENIA GLLAGSASPG ANM AYELTT PIEAVAGDLL AYEFIAVGGT HTMRGRDFNL PDNDGAPIGN VGATRSLSTP SLPPATLDKA DVTWTDNVPR VGIA VDTGT GSDHHDPQVE FFEKPVAIPV PAWCDRIDAI VTGKGGEGAD GFLGFYGNPG QPGSVNTVTW TRGEHFSGTT TILEW DGAE LSIPGFEVSA ANGSNGSGQR PVALGKPVGK GIEEVEYNGL KLAAGGDQHA YGGAGTKPGG GGNGGHWLGI YTQGGP GGP ACAAVQFRKG ALPGEVVGDG EGDVTPPNVS ALHVDVSATS TSITITPSGA VDDA

UniProtKB: Minor tail protein

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Macromolecule #8: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 24.772268 KDa
SequenceString: MSLKVGGLDV VGVFVGDAAA TIYVGAMRIW PPVPDFTPFT ISSEDPGYED LIDEQVPEGA SGCWVTLGGA GGGGGSGRRA NSGYRYGGG GGGGGGYIDR VWIPRASLGS TFTLIRGLGG AGGARAAGSS NGNNGAPGGS TVFSSGSVSL TASGGAAGVK G TSSSASGS ...String:
MSLKVGGLDV VGVFVGDAAA TIYVGAMRIW PPVPDFTPFT ISSEDPGYED LIDEQVPEGA SGCWVTLGGA GGGGGSGRRA NSGYRYGGG GGGGGGYIDR VWIPRASLGS TFTLIRGLGG AGGARAAGSS NGNNGAPGGS TVFSSGSVSL TASGGAAGVK G TSSSASGS GGAGGTTSIS GVSATGYTGG KGGNGGSSPS SGQSRTDGSG AGGGGGGGVR SNDNSFSGGS NGTSSGPAGN GG RGTDGSI NTGGSNAGSG GDGYVLIEWE

UniProtKB: Minor tail protein

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Macromolecule #9: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 11.315524 KDa
SequenceString:
MIDADDYTVN LTSHTTLANI PSGAIIAVSE SLTGKSVTSA GWVKADPTVF PEVTGDTGEA VIVYKHTGTA STSTLLSYHD SPTYQFVIP NGSDIRVIWP TDGFIRF

UniProtKB: Minor tail protein

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Macromolecule #10: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 54.931043 KDa
SequenceString: MPSGLRGYNV YRNGVRQNTS PVTELGSVTI TGLTPGTDYS SQITVTAIDM AGNESEPKTL AELEAEAATD ELSPADPLAP AVRAQIDAL VAAKMKPTSG KEADGAMVGI ETPTGSYYKA YGGDRTKNQP LFLEQNFRYG SCSKMACNTL LLREIDRGHV D WDDTLDQF ...String:
MPSGLRGYNV YRNGVRQNTS PVTELGSVTI TGLTPGTDYS SQITVTAIDM AGNESEPKTL AELEAEAATD ELSPADPLAP AVRAQIDAL VAAKMKPTSG KEADGAMVGI ETPTGSYYKA YGGDRTKNQP LFLEQNFRYG SCSKMACNTL LLREIDRGHV D WDDTLDQF IDGIPNGDKI TVRYLLLFQD GLKDWLQGDP AVQQTYFLNP TLNYDPLAYI RASTPVFEPG TDSHYSNAAT LL MGKILEW CDAEFYTGRS ARELIVEEWK NTVGMESLHW PTTNYMNQPY VRGWTPNMAL PQIQAILGPF AFLAGLLGYP TSK DLEWTA VSTTWSDAAG SLAGNMEDFV KFGKALYEGE FLSEEMNQLR KEIFTRYVEY EPAGPHQGPG WMGFGLNSIC WGHW LGWVG NLGGYIAVLF YNQDDGSVIA TMLNNFAGHA DAVDLFYQIA YLLNPESTGH RDWIFRPDPA EDADEVRDPT LYLTV ESTG DNQIPADVPF EI

UniProtKB: Minor tail protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
1.0 mMMgSO4Magnesium sulfate
68.44 mMNaClSodium chloride
1.0 mMCaCl2Calcium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22280
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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