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- PDB-5ngm: 2.9S structure of the 70S ribosome composing the S. aureus 100S c... -

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Entry
Database: PDB / ID: 5ngm
Title2.9S structure of the 70S ribosome composing the S. aureus 100S complex
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • Ribosome hibernation promoting factor
KeywordsRIBOSOME / Ribosome Cryo-EM Structural Biology Hibernation / Ribosome
Function / homologyRibosomal protein L17 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L25, C-terminal ...Ribosomal protein L17 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein S21 superfamily / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein S12/S23 / Ribosomal protein S7 domain superfamily / Ribosomal protein L23 / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein S14p/S29e / Ribosomal protein S7p/S5e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S10 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L6 / Ribosomal protein L15 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, type Z / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L31 type B / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L5, C-terminal / Ribosome hibernation promotion factor-like / Ribosomal protein L29/L35 superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L24 signature. / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Ribosomal protein S10p/S20e / Ribosomal protein S17 / Ribosomal protein S4/S9 / Ribosomal protein L15 signature. / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S18 signature. / Ribosomal protein S19 signature. / Ribosomal protein L5 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L6 signature 1. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L13 signature. / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein L20 signature. / Ribosomal protein L35 signature. / Ribosomal protein L36 signature. / Ribosomal protein L34 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein S14 signature. / Ribosomal protein S13 signature. / Ribosomal protein S4 signature. / Ribosomal protein L16 signature 1.
Function and homology information
Specimen sourceStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.9 Å resolution
AuthorsMatzov, D. / Aibara, S. / Zimmerman, E. / Bashan, A. / Amunts, A. / Yonath, A.
CitationJournal: Nat Commun / Year: 2017
Title: The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Authors: Donna Matzov / Shintaro Aibara / Arnab Basu / Ella Zimmerman / Anat Bashan / Mee-Ngan F Yap / Alexey Amunts / Ada E Yonath
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 18, 2017 / Release: Oct 4, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 4, 2017Structure modelrepositoryInitial release
1.1Oct 11, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
Aa: 16S ribosomal RNA
Ab: 30S ribosomal protein S2
Ac: 30S ribosomal protein S3
Ad: 30S ribosomal protein S4
Ae: 30S ribosomal protein S5
Af: 30S ribosomal protein S6
Ag: 30S ribosomal protein S7
Ah: 30S ribosomal protein S8
Ai: 30S ribosomal protein S9
Aj: 30S ribosomal protein S10
Ak: 30S ribosomal protein S11
Al: 30S ribosomal protein S12
Am: 30S ribosomal protein S13
An: 30S ribosomal protein S14 type Z
Ao: 30S ribosomal protein S15
Ap: 30S ribosomal protein S16
Aq: 30S ribosomal protein S17
Ar: 30S ribosomal protein S18
As: 30S ribosomal protein S19
At: 30S ribosomal protein S20
Au: 30S ribosomal protein S21
Av: Ribosome hibernation promoting factor
AA: 23S Ribosomal RNA
AB: 5S Ribosomal RNA
AC: 50S ribosomal protein L2
AD: 50S ribosomal protein L3
AE: 50S ribosomal protein L4
AF: 50S ribosomal protein L5
AG: 50S ribosomal protein L6
AH: 50S ribosomal protein L13
AI: 50S ribosomal protein L14
AJ: 50S ribosomal protein L15
AK: 50S ribosomal protein L16
AL: 50S ribosomal protein L17
AM: 50S ribosomal protein L18
AN: 50S ribosomal protein L19
AO: 50S ribosomal protein L20
AP: 50S ribosomal protein L21
AQ: 50S ribosomal protein L22
AR: 50S ribosomal protein L23
AS: 50S ribosomal protein L24
AT: 50S ribosomal protein L25
AU: 50S ribosomal protein L27
AV: 50S ribosomal protein L28
AW: 50S ribosomal protein L29
AX: 50S ribosomal protein L30
AY: 50S ribosomal protein L31 type B
AZ: 50S ribosomal protein L32
A1: 50S ribosomal protein L33
A2: 50S ribosomal protein L34
A3: 50S ribosomal protein L35
A4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,170,506257
Polyers2,165,52452
Non-polymers4,983205
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules AaAAAB

#1: RNA chain 16S ribosomal RNA /


Mass: 502975.906 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1133392934
#23: RNA chain 23S Ribosomal RNA /


Mass: 946697.625 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 610395799
#24: RNA chain 5S Ribosomal RNA /


Mass: 36974.945 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1130374198

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30S ribosomal protein ... , 20 types, 20 molecules AbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAu

#2: Protein/peptide 30S ribosomal protein S2 /


Mass: 29136.369 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UDU1
#3: Protein/peptide 30S ribosomal protein S3 /


Mass: 24143.867 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UU26
#4: Protein/peptide 30S ribosomal protein S4 /


Mass: 23051.416 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TVK2
#5: Protein/peptide 30S ribosomal protein S5 /


Mass: 17770.512 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUC9
#6: Protein/peptide 30S ribosomal protein S6 /


Mass: 11613.146 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TPC6
#7: Protein/peptide 30S ribosomal protein S7 /


Mass: 17826.555 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VHU6
#8: Protein/peptide 30S ribosomal protein S8 /


Mass: 14854.315 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U8T8
#9: Protein/peptide 30S ribosomal protein S9 /


Mass: 14856.987 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0K7UQP6
#10: Protein/peptide 30S ribosomal protein S10 /


Mass: 11598.503 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0H2K0A0
#11: Protein/peptide 30S ribosomal protein S11 /


Mass: 13907.978 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKD6
#12: Protein/peptide 30S ribosomal protein S12 /


Mass: 15320.870 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U1C6
#13: Protein/peptide 30S ribosomal protein S13 /


Mass: 13747.919 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U8U6
#14: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome


Mass: 7317.769 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGW7
#15: Protein/peptide 30S ribosomal protein S15 /


Mass: 10634.330 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U6H8
#16: Protein/peptide 30S ribosomal protein S16 /


Mass: 10253.886 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U6K4
#17: Protein/peptide 30S ribosomal protein S17 /


Mass: 10196.888 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VLD5
#18: Protein/peptide 30S ribosomal protein S18 /


Mass: 9332.018 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UZF4
#19: Protein/peptide 30S ribosomal protein S19 /


Mass: 10639.309 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V0P8
#20: Protein/peptide 30S ribosomal protein S20 /


Mass: 9039.472 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8UXC3
#21: Protein/peptide 30S ribosomal protein S21 /


Mass: 6994.267 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UHS1

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50S ribosomal protein ... , 28 types, 28 molecules ACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZA1A2A3A4

#25: Protein/peptide 50S ribosomal protein L2 /


Mass: 30217.164 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077W1J0
#26: Protein/peptide 50S ribosomal protein L3 /


Mass: 23760.256 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U3W0
#27: Protein/peptide 50S ribosomal protein L4 /


Mass: 22495.697 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRC7
#28: Protein/peptide 50S ribosomal protein L5 /


Mass: 20296.637 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUC3
#29: Protein/peptide 50S ribosomal protein L6 /


Mass: 19818.580 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U3X2
#30: Protein/peptide 50S ribosomal protein L13 /


Mass: 16359.427 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUE6
#31: Protein/peptide 50S ribosomal protein L14 /


Mass: 13157.342 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UUA0
#32: Protein/peptide 50S ribosomal protein L15 /


Mass: 15628.890 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGA7
#33: Protein/peptide 50S ribosomal protein L16 /


Mass: 16274.049 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V4G0
#34: Protein/peptide 50S ribosomal protein L17 /


Mass: 13771.773 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UG91
#35: Protein/peptide 50S ribosomal protein L18 /


Mass: 13124.093 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRE0
#36: Protein/peptide 50S ribosomal protein L19 /


Mass: 13392.771 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UVB6
#37: Protein/peptide 50S ribosomal protein L20 /


Mass: 13720.295 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VMP6
#38: Protein/peptide 50S ribosomal protein L21 /


Mass: 11354.081 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: D7URR3
#39: Protein/peptide 50S ribosomal protein L22 /


Mass: 12857.922 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKF9
#40: Protein/peptide 50S ribosomal protein L23 /


Mass: 10625.398 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUB4
#41: Protein/peptide 50S ribosomal protein L24 /


Mass: 11561.504 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRD5
#42: Protein/peptide 50S ribosomal protein L25 / / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133Q8Z9
#43: Protein/peptide 50S ribosomal protein L27 /


Mass: 10334.798 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0U1N012
#44: Protein/peptide 50S ribosomal protein L28 /


Mass: 6995.289 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077URJ8
#45: Protein/peptide 50S ribosomal protein L29 /


Mass: 8592.900 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0H3KED7
#46: Protein/peptide 50S ribosomal protein L30 /


Mass: 6565.683 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8UVN7
#47: Protein/peptide 50S ribosomal protein L31 type B / Ribosome


Mass: 9737.912 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRP5
#48: Protein/peptide 50S ribosomal protein L32 /


Mass: 6500.609 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UWR7
#49: Protein/peptide 50S ribosomal protein L33 /


Mass: 5944.937 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V2P0
#50: Protein/peptide 50S ribosomal protein L34 /


Mass: 5454.642 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YZB6
#51: Protein/peptide 50S ribosomal protein L35 /


Mass: 7722.368 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UL47
#52: Protein/peptide 50S ribosomal protein L36 /


Mass: 4318.422 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGV8

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Protein/peptide / Non-polymers , 2 types, 206 molecules Av

#22: Protein/peptide Ribosome hibernation promoting factor / HPF


Mass: 22244.914 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8USK0
#53: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 205 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
170S ribosome of the S. aureus 100S complexRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 520NATURAL
230S subunitCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 221NATURAL
316S rRNACOMPLEX12NATURAL
430S ribosomal proteinsCOMPLEX2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 212NATURAL
550S subunitCOMPLEX23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 521NATURAL
623S and 5S rRNACOMPLEX23, 245NATURAL
750S ribosomal proteinsCOMPLEX25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 525NATURAL
Molecular weight
IDEntity assembly IDExperimental value
11NO
12
13
14
15
16
17
Source (natural)
IDEntity assembly IDNcbi tax IDOrganismStrain
211280Staphylococcus aureus (bacteria)USA300_FPR3757
321280Staphylococcus aureus (bacteria)USA300_FPR3757
431280Staphylococcus aureus (bacteria)USA300_FPR3757
541280Staphylococcus aureus (bacteria)USA300_FPR3757
651280Staphylococcus aureus (bacteria)USA300_FPR3757
761280Staphylococcus aureus (bacteria)USA300_FPR3757
871280Staphylococcus aureus (bacteria)USA300_FPR3757
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 224554 / Symmetry type: POINT

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