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- EMDB-30821: Structure of Wild-type PSI monomer2 from Cyanophora paradoxa -

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Basic information

Entry
Database: EMDB / ID: EMD-30821
TitleStructure of Wild-type PSI monomer2 from Cyanophora paradoxa
Map data
Sample
  • Complex: PSI monomer2
    • Protein or peptide: x 10 types
  • Ligand: x 7 types
KeywordsPhotosystem I / ELECTRON TRANSPORT / PHOTOSYNTHESIS
Function / homology
Function and homology information


cyanelle thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding ...cyanelle thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD ...Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit II, cyanelle
Similarity search - Component
Biological speciesCyanophora paradoxa (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKato K / Nagao R
CitationJournal: Biorxiv / Year: 2022
Title: Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Authors: Kato K / Nagao R / Ueno Y / Yokono M / Suzuki T / Jiang TY / Dohmae N / Akita F / Akimoto S / Miyazaki N / Shen JR
History
DepositionDec 25, 2020-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dr1
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30821.png

Downloads & links

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Map

FileDownload / File: emd_30821.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 400 pix.
= 437.2 Å		1.09 Å/pix.
x 400 pix.
= 437.2 Å		1.09 Å/pix.
x 400 pix.
= 437.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.093 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.29245728 - 0.37572888
Average (Standard dev.)0.00037496208 (±0.0060401647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 437.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0931.0931.093
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z437.200437.200437.200
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2920.3760.000

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Supplemental data

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Sample components

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Entire : PSI monomer2

EntireName: PSI monomer2
Components
  • Complex: PSI monomer2
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II, cyanelle
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: PSI monomer2

SupramoleculeName: PSI monomer2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 83.397305 KDa
SequenceString: MRISPPEREA KKVKIVIDKD PVSTSFDKWA VPGHFSRTLA KGPKTTTWIW NLHADVHDFD SYTSDLEEVS RKIFSAHFGH LAVVFIWLS GAYFHGARFS NYEAWLSNPT TIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGLFQMWR ASGITTELQL Y VTAIGALV ...String:
MRISPPEREA KKVKIVIDKD PVSTSFDKWA VPGHFSRTLA KGPKTTTWIW NLHADVHDFD SYTSDLEEVS RKIFSAHFGH LAVVFIWLS GAYFHGARFS NYEAWLSNPT TIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGLFQMWR ASGITTELQL Y VTAIGALV MAALMLFAGW FHYHKAAPKL EWFQNAESMM NHHLGGLFGL GSLSWAGHQI HVSLPVNKLL DSGVSPQEIP LP HEFILNK DLIAQLYPSF GQGLTPFFTL NWNEYSDFLT FKGGLNPVTG GLWLSDSAHH HLAIAVLFIV AGHMYRTNWG IGH SMKEMY DSHKGPFTGE GHKGVYEIFT NSWHAQLSLN LALFGSLSII VAHHMYSMPP YPYLATDYAT SLCLFTHHVW IGGF LIVGA GAHAAIFMVR DYDPAQNYNN LVDRVLRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMRAL GRPQDMFSDA AIQLQ PVFA QWVQGVNSAA AGNTAPNALA NASYAFGGDI VSVGGKVAMM PISLGTADFL VHHIHAFTIH VTVLILLKGV LFARNS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SVVLFHFSWK MQSDVWGNVT ADGAVSHITG NNFAQGA IT INGWLRDFLW AQASQVIQSY GSALSAYGLM FLGAHFIWAF SLMFLFSGRG YWQELIESIV WAHNKLKFAP SIQPRALS I TQGRAVGVAH YLLGGIATTW SFFHARIISV G

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 82.316312 KDa
SequenceString: MGTKFPKASQ ALAQDPTTRR IWYGIATAND FETNDGITEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVKD PLNTRPIAH AISDPHFGQR AIEAFSQAGA SSPVNISYSG VYQWWYTQGM RTNEELYNGA IFLLILSALS LFAGWLHLQP K FRPNLSWF ...String:
MGTKFPKASQ ALAQDPTTRR IWYGIATAND FETNDGITEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVKD PLNTRPIAH AISDPHFGQR AIEAFSQAGA SSPVNISYSG VYQWWYTQGM RTNEELYNGA IFLLILSALS LFAGWLHLQP K FRPNLSWF KNAESRLNHH LGGLFGTSSL AWTGHIVHVA IPESRGQHVG WDNFLQVAPH PAGLQPFFTG NWGVYTENPD TA NHVFGSS DGAGTAILTF LGGFHPQTQS LWLTDIAHHH LAIAVLFIVA GHMYRTNFGI GHSIKEILNG HRPPGGRLGA GHV GLYDTV NNSLHFQLGL ALAALGVITS LVAQHMYSIP PYAYLARDFT TQAALYTHHQ YIAGFLMVGA FAHGAIFLVR DYDA EQNKN NVLARIIDHK EAIISHLSWV SLFLGFHTLG LYVHNDVVQA FGTPEKQILI EPVFAQWIQS VHGKSLYGFE VLLNN ADSI TRVAPGSAQP IWLPGWLDAI NSGNNSLFLT IGPGDFLVHH AIALGLHTTT LILVKGALDA RGSKLMPDKK DFGYSF PCD GPGRGGTCDI SAWDAFYLAV FWMLNTIGWT TFYWHWKHLG VWQGNVAQFN ESSTYLMGWF RDYLWLNSSQ LINGYNP FG MNNLSVWAWM FLFGHLIWAT GFMFLISWRG YWQELIETLV WAHERTPLAN LVRWKDKPVA LSIVQARLVG LAHFAVGY I VTYAAFLIAS TASKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 8.850221 KDa
SequenceString:
MAHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCRANQIA SAPRTEDCVG CKRCESACPT DFLSIRVYLG AETTRSMGLG Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II, cyanelle

MacromoleculeName: Photosystem I reaction center subunit II, cyanelle / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 23.693258 KDa
SequenceString: MNAFVASVAP IAVAGSATLS SAVCAQKKAF FGAQVAAKKT TFEAAPARFI VRAEEEEAAP AEKVEKKAAA PKPFSVPTLN LNAPTPIFG GSTGGLLRKA EVEEFYSITW TGKSETVFEL PTGGAAIMRA GENLLRLARK EQCIALGAQL KDKFKITDYK I YRVYPSGE ...String:
MNAFVASVAP IAVAGSATLS SAVCAQKKAF FGAQVAAKKT TFEAAPARFI VRAEEEEAAP AEKVEKKAAA PKPFSVPTLN LNAPTPIFG GSTGGLLRKA EVEEFYSITW TGKSETVFEL PTGGAAIMRA GENLLRLARK EQCIALGAQL KDKFKITDYK I YRVYPSGE VQFLHPKDGV FPEKVNPGRV AVGSNKRRIG QNPDPAKLKF KGQETFDSDL KL

UniProtKB: Photosystem I reaction center subunit II, cyanelle

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 8.058164 KDa
SequenceString:
MVQRGSKVRI LRKESYWYQE IGTVASIDQS GIKYPVIVRF EKVNYSNVNS NNFSLDEVVE VEPPPSKKKA

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 20.697777 KDa
SequenceString:
MRKLFLLMFC LSGLILTTDI RPVRADVAGL IPCSQSDAFE RRLKNTTQRL ENRLKKYEPG SAPAEALQKQ IDKTQQRFDK YRNSGLLCG ADGLPHLITD GRWSHAGEFT IPGLLFLYIA GFIGWSGRSY LQAVAASDNS TEKEIIIDIP VALQSVSKGF V WPLAALQE FSSGKLTARD EEITISPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 3.77262 KDa
SequenceString:
MVSNLPSILV PMVGIVLPAI VMALLFVYIE TDEIA

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 4.483274 KDa
SequenceString:
MSFSKYLSTA PVIGTLTAFF LAGLLIEINR FNPDLLVYPF

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 15.376591 KDa
SequenceString:
MAKDAVKPFY DDAFIGHLST PISNSSAVNG LLANLPAYRK GLTPRLRGLE IGMAHGYFLT GPFVELGPLR NTDGGILYGS LSAVGLVVI LTACLALYGK ANFSGSSKSK DATLWESGEG WSDFVSGWLI GGAGSVGFAY LLLQYIL

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Macromolecule #10: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 3.334065 KDa
SequenceString:
MLADGQIFTA LAVALVPGIL ALRLALELYK F

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #11: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 11 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 80 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #13: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 13 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 19 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 16 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #17: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 17 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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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

Concentration0.007 mg/mL
BufferpH: 6.5 / Component:
ConcentrationFormula
50.0 mMMES-NaOH
0.03 %DDM
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1603082
Startup modelType of model: OTHER / Details: De novo generation
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 110380
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationSoftware - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7dr1:
Structure of Wild-type PSI monomer2 from Cyanophora paradoxa

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