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- EMDB-19970: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 b... -

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Basic information

Entry
Database: EMDB / ID: EMD-19970
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - core, and wedge module proteins
Map dataPhage phi812 baseplate in the pre-contraction state - core, wedge modules; postprocessed map
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Complex: Tail
      • Complex: Baseplate
        • Protein or peptide: Peptidase C51 domain-containing protein
        • Protein or peptide: TmpF
        • Protein or peptide: Baseplate wedge subunit
        • Protein or peptide: Baseplate component
        • Protein or peptide: Putative baseplate component
        • Protein or peptide: Baseplate component
        • Protein or peptide: GP-PDE domain-containing protein
        • Protein or peptide: NlpC/P60 domain-containing protein
Keywordsbacteriophage / phage / contractile / phi812 / baseplate / VIRUS
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / phosphoric diester hydrolase activity / cysteine-type peptidase activity / lipid metabolic process
Similarity search - Function
: / Putative phage tail tube initiator protein / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / CHAP domain profile. / CHAP domain / CHAP domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. ...: / Putative phage tail tube initiator protein / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / CHAP domain profile. / CHAP domain / CHAP domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Baseplate protein J-like / Baseplate J-like protein barrel domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / LysM domain superfamily / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Baseplate component / Baseplate wedge subunit / NlpC/P60 domain-containing protein / Baseplate component / GP-PDE domain-containing protein / TmpF / Peptidase C51 domain-containing protein / Putative baseplate component
Similarity search - Component
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsBinovsky J / Siborova M / Baska R / Pichel-Beleiro A / Skubnik K / Novacek J / van Raaij MJ / Plevka P
Funding supportEuropean Union, Czech Republic, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky J / Siborova M / Baska R / Pichel-Beleiro A / Skubnik K / Novacek J / van Raaij MJ / Plevka P
History
DepositionMar 27, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19970.png

Downloads & links

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Map

FileDownload / File: emd_19970.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage phi812 baseplate in the pre-contraction state - core, wedge modules; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 322.5 Å		1.08 Å/pix.
x 300 pix.
= 322.5 Å		1.08 Å/pix.
x 300 pix.
= 322.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.075 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.13163494 - 0.18665607
Average (Standard dev.)0.0007822496 (±0.0104716085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 322.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19970_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage phi812 baseplate in the pre-contraction state -...

Fileemd_19970_half_map_1.map
AnnotationPhage phi812 baseplate in the pre-contraction state - core, wedge modules; half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage phi812 baseplate in the pre-contraction state -...

Fileemd_19970_half_map_2.map
AnnotationPhage phi812 baseplate in the pre-contraction state - core, wedge modules; half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Staphylococcus phage 812

EntireName: Staphylococcus phage 812 (virus)
Components
  • Virus: Staphylococcus phage 812 (virus)
    • Complex: Tail
      • Complex: Baseplate
        • Protein or peptide: Peptidase C51 domain-containing protein
        • Protein or peptide: TmpF
        • Protein or peptide: Baseplate wedge subunit
        • Protein or peptide: Baseplate component
        • Protein or peptide: Putative baseplate component
        • Protein or peptide: Baseplate component
        • Protein or peptide: GP-PDE domain-containing protein
        • Protein or peptide: NlpC/P60 domain-containing protein

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Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Supramolecule #2: Tail

SupramoleculeName: Tail / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Staphylococcus phage 812 (virus)

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Supramolecule #3: Baseplate

SupramoleculeName: Baseplate / type: complex / ID: 3 / Parent: 2 / Macromolecule list: all
Source (natural)Organism: Staphylococcus phage 812 (virus)

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Macromolecule #1: Peptidase C51 domain-containing protein

MacromoleculeName: Peptidase C51 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 91.364289 KDa
SequenceString: MRRIRRPKVR IEIVTDDNTF TLRFEDTRDY NGDEFGAKLL GFQTKNSMED DSSVFQINMA GDTYWDKLVM ANDIIRIFIT PNDDPNDKE GKQERLIQVG MVSQVSKVGS YGNDQTQFRI TGQSFVKPFM KFGLGVIQEV QAVLPEVGWL IDGDGDNEVK F TGSSAHEV ...String:
MRRIRRPKVR IEIVTDDNTF TLRFEDTRDY NGDEFGAKLL GFQTKNSMED DSSVFQINMA GDTYWDKLVM ANDIIRIFIT PNDDPNDKE GKQERLIQVG MVSQVSKVGS YGNDQTQFRI TGQSFVKPFM KFGLGVIQEV QAVLPEVGWL IDGDGDNEVK F TGSSAHEV MTGIIRRFIP YMKYNYTEKT YNTIDNYLDY DDLSSWDEFE KLTEVSAFTN FDGSLKQLMD MVTARPFNEL FF KNSEKTP GKAQLVLRKT PFNPTEWRAL DMIKVPTEDF IEEDVGKSDV ETYSIFTATP AGMLKELNGD VFSKPQFHPE LTD RYGYTK FEVENIYLST KSGSATEDSD SSGDDNGTER GTYSKIMKDL SNYGRDNISK GIDKYTSKLS SKYKNLKKAQ AKKI IEKFV KEGKVTEKEY EKITGNKVDD ELTSDNRPKL TKDKLKSILK EKFKTQDDFN NSKKKKKAKT DALKELTTKY RFGNK THAT TLLDEYIKYK GEPPNDEAFD KYLKAIEGVS NVATDTGSDA SDSPLVMFSR MLFNWYHGNP NFYAGDIIVL GDPKYD LGK RLFIEDKQRG DTWEFYIESV EHKFDYKQGY YTTVGVTRGL KDAILEDGKG SPHRFAGLWN QSSDFMGGLM GEDTSKE LK EKGVAEKQSS GDKDGGSDSG GAQDGGSLDS LKKYNGKLPK HDPSFVQPGN RHYKYQCTWY AYNRRGQLGI PVPLWGDA A DWIGGAKGAG YGVGRTPKQG ACVIWQRGVQ GGSPQYGHVA FVEKVLDGGK KIFISEHNYA TPNGYGTRTI DMSSAIGKN AQFIYDKK

UniProtKB: Peptidase C51 domain-containing protein

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Macromolecule #2: TmpF

MacromoleculeName: TmpF / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 116.389945 KDa
SequenceString: MANFLKNLHP LLRRDRNKKD NQDPNFALID ALNEEMNQVE KDAIESKLQS SLKTSTSEYL DKFGDWFGVY RKTDEKDDVY RARIIKYLL LKRGTNNAII DAIKDYLGRD DIDVSVYEPF TNIFYTNKSH LNGEDHLMGY YYRFAVINVS IGDYFPVEII D VINEFKPA ...String:
MANFLKNLHP LLRRDRNKKD NQDPNFALID ALNEEMNQVE KDAIESKLQS SLKTSTSEYL DKFGDWFGVY RKTDEKDDVY RARIIKYLL LKRGTNNAII DAIKDYLGRD DIDVSVYEPF TNIFYTNKSH LNGEDHLMGY YYRFAVINVS IGDYFPVEII D VINEFKPA GVTLYVTYDG ASTIRGGAII KWLDGLPKIE TYQEFDRFTG YDDTFYGHIN MNQSKDTDNS SSDIFKTNHS LI NSLDVLT GSSSVGRQYI NYGYVTSYVY NPGMTSSVNQ ISASTEGRGQ EVPTDYYMYT STKNNNTVEL SMQTTSGVSY LYN NFNFRD YMSKYRPQVD LQSDEARRIV SDYIKELSID YYLSAVIPPD ESIEIKLQVY DFSINRWLTV SINNLSFYEK NIGS NIGYI KDYLNSELNM FTRLEINAGK RDSVDIKVNY LDLMFYYYER GIYTIKPYKA LIENYLDISR ETYVEAFKIA SLSNG DIIT KTGFQPIGYL KLVGNYENTI PSTINIVAKD TDNNPIESNE LDVYNTVENR NLLQSYKGVN TIAREITSTK EFTVSG WAK EIYSTNYLSK VLKPGKVYTL SFDMEITGND PTLKSYSDNH GIYLYSNTKG IVVNGVKSME RTIGNKVSVT QTFTAPT IT DHRLLIYTGR YTSDGKASTP PVFFNTVKIT ELKLTEGSSK LEYSPAPEDK PNVIEKGIKF NNILTNIQTL SINSDTIL K NVTLYYSYYG DSWVELKTLG NISTGETTET NNLIDLYGLQ TVDYSNINPM SKVSLRSIWN VKLGELNNQE GSLSNMPND YFNAVWQDID KLSDIELGSM RMVKDTEGGV FDGATGEIIK ATLFNVGAYT DLDMLAYTLT NYTEPLTLGS SRLISELKEE LLTSESFNV DNRIKVIDSI YEELPNTSII KNGFVEREVT GSKYLDYGLY EPIEDGTRYK LIVEGEFKDN IEFISLYNSN P NFNETFIY PSEIINGVAE KEFIAKPSTE DKPRLNTDVR IYIRPYDSTI SKVRRVELRK V

UniProtKB: TmpF

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Macromolecule #3: Baseplate wedge subunit

MacromoleculeName: Baseplate wedge subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 26.611752 KDa
SequenceString: MRFKKHVVQH EETMQAIAQR YYGDVSYWID LVEHNNLKYP YLVETDEEKM KDPERLASTG DTLIIPIESD LTDVSAKEIN SRDKDVLVE LALGRDLNIT ADEKYFNEHG TSDNILAFST NGNGDLDTVK GIDNMKQQLQ ARLLTPRGSL MLHPNYGSDL H NLFGLNIP ...String:
MRFKKHVVQH EETMQAIAQR YYGDVSYWID LVEHNNLKYP YLVETDEEKM KDPERLASTG DTLIIPIESD LTDVSAKEIN SRDKDVLVE LALGRDLNIT ADEKYFNEHG TSDNILAFST NGNGDLDTVK GIDNMKQQLQ ARLLTPRGSL MLHPNYGSDL H NLFGLNIP EQATLIEMEV LRTLTSDNRV KSANLIDWKI QGNVYSGQFS VEIKSVEESI NFVLGQDEEG IFALFE

UniProtKB: Baseplate wedge subunit

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Macromolecule #4: Baseplate component

MacromoleculeName: Baseplate component / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 19.998748 KDa
SequenceString:
MNNFIPQPQG LLRFLNTLDT DLTSSHMNLL DEEVSFVSKF YTPQLQLSEL AKKVLTNIKT DDIPVLEREF NDNTIIHKAN DTLLKVQAP RMYMILQSIV LEAYAIVNCF VENPSSLKYL TEEDVSITRE NLNYVADYLG NYDDYNSVVL DLRDLDLCFS A IELQLPLI KKEANV

UniProtKB: Baseplate component

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Macromolecule #5: Putative baseplate component

MacromoleculeName: Putative baseplate component / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 29.381604 KDa
SequenceString: MPQSDGISNL HRIALRFPKE GGGYDMYRFK VNPENYTIDS PQRTTAIKTK SDIVIEDYGK DIEVINFTGT TGFRPVREAD GLKTGKQKM EELQSRVSEY AMQGGSGNVS GSYLQFFNFT DDSYYKVHLA PQGLKITRSK DEPLLFRYEI TLVVIGSLTE A DRSAVTTE ...String:
MPQSDGISNL HRIALRFPKE GGGYDMYRFK VNPENYTIDS PQRTTAIKTK SDIVIEDYGK DIEVINFTGT TGFRPVREAD GLKTGKQKM EELQSRVSEY AMQGGSGNVS GSYLQFFNFT DDSYYKVHLA PQGLKITRSK DEPLLFRYEI TLVVIGSLTE A DRSAVTTE EFGNVKPNAS QRVDEGIKEL DKNARKTRDR NNQEISRREN TIPKSTGDNT NEGNRLKQSF PSSSIYNPRQ ST NGLKGNI DNMALIIGYG DGGVSS

UniProtKB: Putative baseplate component

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Macromolecule #6: Baseplate component

MacromoleculeName: Baseplate component / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 39.248859 KDa
SequenceString: MKTRKLTNIL SKLIDKTMAG TSKITDFTPG SASRSLLEAV SLEIEQFYIL TKENIDWGIQ EGIIEAFDFQ KRQSKRAYGD VTIQFYQPL DMRMYIPAGT TFTSTRQEYP QQFETLVDYY AEPDSTEIVV EVYCKETGVA GNVPEGTINT IASGSSLIRS V NNEYSFNT ...String:
MKTRKLTNIL SKLIDKTMAG TSKITDFTPG SASRSLLEAV SLEIEQFYIL TKENIDWGIQ EGIIEAFDFQ KRQSKRAYGD VTIQFYQPL DMRMYIPAGT TFTSTRQEYP QQFETLVDYY AEPDSTEIVV EVYCKETGVA GNVPEGTINT IASGSSLIRS V NNEYSFNT GTKEESQEDF KRRFHSFVES RGRATNKSVR YGALQIPDVE GVYVYEETGH ITVFAHDRNG NLSDTLKEDI ID ALQDYRP SGIMLDVTGV EKEEVNVSAT VTISNKSRIG DTLQKHIESV IRSYLNNLKT SDDLIITDLI QAIMNIDDVL IYD VSFDNL DENIIVPPQG IIRAGEIKVE LK

UniProtKB: Baseplate component

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Macromolecule #7: GP-PDE domain-containing protein

MacromoleculeName: GP-PDE domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 96.199547 KDa
SequenceString: MVVRFQSSMG RSLKRVDSDD LNVKGLVLAT VSKINYKYQS VEVKVNNLTL GSRIGDDGSL AVPYPKSFIG RTPEGSVFGT KPLITEGSV VLIGFLNDDI NSPIILSVYG DNEQNKMINT NPLDGGKFDT ESVYKYSSSL YEILPSLNYK YDDGEGTSIR T YNGKSFFS ...String:
MVVRFQSSMG RSLKRVDSDD LNVKGLVLAT VSKINYKYQS VEVKVNNLTL GSRIGDDGSL AVPYPKSFIG RTPEGSVFGT KPLITEGSV VLIGFLNDDI NSPIILSVYG DNEQNKMINT NPLDGGKFDT ESVYKYSSSL YEILPSLNYK YDDGEGTSIR T YNGKSFFS MTSGEEEKPQ ATDFYTGTEY QDLFTSYYGN KTLIEPRIQK APNMLFKHQG VFYDDGTPDN HITTLFISER GD IRASVLN TETQKRTTQE MSSDGSYRVI KQDDDLMLDE AQVWIEYGIS EDNKFYIKND KHKFEFTDEG IYIDDKPMLE NLD ESIAEA MKNLNEIQKE LDDINYLLKG VGKDNLEELI ESTKESIEAS KKATSDVNRL TTQIAEVSGR TEGIITQFQK FRDE TFKDF YEDASTVINE VNQNFPTMKT DVKTLKTKVD NLEKTEIPNI KTRLTELENN NNNADKIISD RGEHIGAMIQ LEENV TVPM RKYMPIPWSK VTYNNAEFWD SNNPTRLVVP KGITKVRVAG NVLWDSNATG QRMLRILKNG TYSIGLPYTR DVAIST APQ NGTSGVIPVK EGDYFEFEAF QDSEGDRQFR ADPYTWFSIE AIELETETME KDFMLIGHRG ATGYTDEHTI KGYQMAL DK GADYIELDLQ LTKDNKLLCM HDSTIDRTTT GTGKVGDMTL SYIQTNFTSL NGEPIPSLDD VLNHFGTKVK YYIETKRP F DANMDRELLT QLKAKGLIGI GSERFQVIIQ SFARESLINI HNQFSNIPLA YLTSTFSESE MDDCLSYGFY AIAPKYTTI TKELVDLAHS KGLKVHAWTV NTKEEMQSLI QMGVDGFFTN YLDEYKKI

UniProtKB: GP-PDE domain-containing protein

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Macromolecule #8: NlpC/P60 domain-containing protein

MacromoleculeName: NlpC/P60 domain-containing protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 34.645887 KDa
SequenceString: MATDKEAKDV IDKFIDNVFN FDVLTKERIK EKDEEIKKIT TDDMYEKVVY IRPYVGVIQS LNPQHVQYES FSNNGYDIEA ELSFRKVSY LVDKGSIPTD SLSTLTVHLV ERNQELLIDY FDEIQDVLYG EYMEEEYVFD EDVPLSTILA LDLNDNLKSL S NIKYMFKG ...String:
MATDKEAKDV IDKFIDNVFN FDVLTKERIK EKDEEIKKIT TDDMYEKVVY IRPYVGVIQS LNPQHVQYES FSNNGYDIEA ELSFRKVSY LVDKGSIPTD SLSTLTVHLV ERNQELLIDY FDEIQDVLYG EYMEEEYVFD EDVPLSTILA LDLNDNLKSL S NIKYMFKG APKENPFGTD KDVYIDTYNL LYWLYLGEDE ELAYPMNINY FFTEGRFFTI FGKGHKYKVD VSKFIVGDIL FF GRSDTNI GIYVGDGEFI SMMGKFPKDE TPIGKYKLDD YWNEFNGRVM RFDEEVYI

UniProtKB: NlpC/P60 domain-containing 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

BufferpH: 8 / Details: 50mM Tris, 10mM NaCl, 10mM CaCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 23421
Startup modelType of model: EMDB MAP
EMDB ID:

8210

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 9705
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: C3 symmetry imposed
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9euh:
Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - core, and wedge module proteins

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