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- PDB-3j9w: Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome ... -

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Entry
Database: PDB / ID: 3j9w
TitleCryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • MifM
  • mRNAMessenger RNA
  • tRNA-Asp
KeywordsRIBOSOME / stalling / translation arrest / mifm / L22
Function / homologyRibosomal protein L15 / Ribosomal protein L22/L17 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L14 superfamily ...Ribosomal protein L15 / Ribosomal protein L22/L17 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L14 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / L28p-like / Ribosomal protein L19 superfamily / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L33 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L20, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L14p/L23e / Ribosomal protein S6, conserved site / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L2, C-terminal / Ribosomal protein L16, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein S7 domain / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L16p/L10e / Ribosomal protein S5 domain 2-type fold / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / KH domain / Ribosomal protein S18 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal L32p protein family / Ribosomal protein S20 / Ribosomal protein L35 / Ribosomal protein S17 signature. / Ribosomal protein S19 signature. / Ribosomal protein S6 / Ribosomal protein L6 signature 1. / Ribosomal protein L16 signature 1. / Ribosomal protein S5 signature. / Ribosomal protein L33 signature. / Ribosomal protein L29 signature. / Ribosomal protein S3 signature. / Ribosomal protein S14 signature. / Ribosomal protein L15 signature.
Function and homology information
Specimen sourceBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSohmen, D. / Chiba, S. / Shimokawa-Chiba, N. / Innis, C.A. / Berninghausen, O. / Beckmann, R. / Ito, K. / Wilson, D.N.
CitationJournal: Nat Commun / Year: 2015
Title: Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Authors: Daniel Sohmen / Shinobu Chiba / Naomi Shimokawa-Chiba / C Axel Innis / Otto Berninghausen / Roland Beckmann / Koreaki Ito / Daniel N Wilson
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 16, 2015 / Release: Apr 29, 2015
RevisionDateData content typeGroupProviderType
1.0Apr 29, 2015Structure modelrepositoryInitial release
1.1May 6, 2015Structure modelDatabase references

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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 uS2
AC: 30S ribosomal protein uS3
AD: 30S ribosomal protein uS4
AE: 30S ribosomal protein uS5
AF: 30S ribosomal protein bS6
AG: 30S ribosomal protein uS7
AH: 30S ribosomal protein uS8
AI: 30S ribosomal protein uS9
AJ: 30S ribosomal protein uS10
AK: 30S ribosomal protein uS11
AL: 30S ribosomal protein uS12
AM: 30S ribosomal protein uS13
AN: 30S ribosomal protein uS14
AO: 30S ribosomal protein uS15
AP: 30S ribosomal protein bS16
AQ: 30S ribosomal protein uS17
AR: 30S ribosomal protein bS18
AS: 30S ribosomal protein uS19
AT: 30S ribosomal protein bS20
AX: tRNA-Asp
AY: mRNA
AZ: MifM
B0: 50S ribosomal protein bL28
B1: 50S ribosomal protein uL29
B2: 50S ribosomal protein uL30
B3: 50S ribosomal protein bL31
B4: 50S ribosomal protein bL32
B5: 50S ribosomal protein bL33
B6: 50S ribosomal protein bL34
B7: 50S ribosomal protein bL35
B8: 50S ribosomal protein bL36
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BD: 50S ribosomal protein uL2
BE: 50S ribosomal protein uL3
BF: 50S ribosomal protein uL4
BG: 50S ribosomal protein uL5
BH: 50S ribosomal protein uL6
BJ: 50S ribosomal protein uL10
BK: 50S ribosomal protein uL11
BM: 50S ribosomal protein uL13
BN: 50S ribosomal protein uL14
BO: 50S ribosomal protein uL15
BP: 50S ribosomal protein uL16
BQ: 50S ribosomal protein bL17
BR: 50S ribosomal protein uL18
BS: 50S ribosomal protein bL19
BT: 50S ribosomal protein bL20
BU: 50S ribosomal protein bL21
BV: 50S ribosomal protein uL22
BW: 50S ribosomal protein uL23
BX: 50S ribosomal protein uL24
BZ: 50S ribosomal protein bL27


Theoretical massNumber of molelcules
Total (without water)2,185,39954
Polyers2,185,39954
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules AAAXAYBABB

#1: RNA chain 16S ribosomal RNA /


Mass: 503698.281 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#21: RNA chain tRNA-Asp


Mass: 24815.682 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#22: RNA chain mRNA / Messenger RNA


Mass: 6204.786 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#33: RNA chain 23S ribosomal RNA /


Mass: 949606.250 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#34: RNA chain 5S ribosomal RNA /


Mass: 38423.863 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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30S ribosomal protein ... , 19 types, 19 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASAT

#2: Protein/peptide 30S ribosomal protein uS2 /


Mass: 28009.297 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21464
#3: Protein/peptide 30S ribosomal protein uS3 /


Mass: 24364.887 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21465
#4: Protein/peptide 30S ribosomal protein uS4 /


Mass: 22874.271 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21466
#5: Protein/peptide 30S ribosomal protein uS5 /


Mass: 17650.625 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21467
#6: Protein/peptide 30S ribosomal protein bS6 /


Mass: 11140.548 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21468
#7: Protein/peptide 30S ribosomal protein uS7 /


Mass: 17915.879 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21469
#8: Protein/peptide 30S ribosomal protein uS8 /


Mass: 14901.427 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12879
#9: Protein/peptide 30S ribosomal protein uS9 /


Mass: 14335.504 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21470
#10: Protein/peptide 30S ribosomal protein uS10 /


Mass: 11687.661 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21471
#11: Protein/peptide 30S ribosomal protein uS11 /


Mass: 13952.000 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P04969
#12: Protein/peptide 30S ribosomal protein uS12 /


Mass: 15248.736 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21472
#13: Protein/peptide 30S ribosomal protein uS13 /


Mass: 13818.085 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20282
#14: Protein/peptide 30S ribosomal protein uS14 /


Mass: 7263.803 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12878
#15: Protein/peptide 30S ribosomal protein uS15 /


Mass: 10597.224 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21473
#16: Protein/peptide 30S ribosomal protein bS16 /


Mass: 10153.833 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21474
#17: Protein/peptide 30S ribosomal protein uS17 /


Mass: 10220.979 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12874
#18: Protein/peptide 30S ribosomal protein bS18 /


Mass: 8990.613 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21475
#19: Protein/peptide 30S ribosomal protein uS19 /


Mass: 10607.309 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21476
#20: Protein/peptide 30S ribosomal protein bS20 /


Mass: 9622.217 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21477

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Protein/peptide , 1 types, 1 molecules AZ

#23: Protein/peptide MifM


Mass: 11156.958 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q7WY64

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50S ribosomal protein ... , 29 types, 29 molecules B0B1B2B3B4B5B6B7B8BDBEBFBGBHBJBKBMBNBOBPBQBRBSBTBUBVBWBXBZ

#24: Protein/peptide 50S ribosomal protein bL28 /


Mass: 6826.144 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#25: Protein/peptide 50S ribosomal protein uL29 /


Mass: 7728.029 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#26: Protein/peptide 50S ribosomal protein uL30 /


Mass: 6650.795 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947
#27: Protein/peptide 50S ribosomal protein bL31 /


Mass: 7458.582 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q03223
#28: Protein/peptide 50S ribosomal protein bL32 /


Mass: 6745.073 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#29: Protein/peptide 50S ribosomal protein bL33 /


Mass: 5915.875 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#30: Protein/peptide 50S ribosomal protein bL34 /


Mass: 5271.332 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#31: Protein/peptide 50S ribosomal protein bL35 /


Mass: 7581.128 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#32: Protein/peptide 50S ribosomal protein bL36 /


Mass: 4318.422 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#35: Protein/peptide 50S ribosomal protein uL2 /


Mass: 30335.125 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#36: Protein/peptide 50S ribosomal protein uL3 /


Mass: 22723.348 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#37: Protein/peptide 50S ribosomal protein uL4 /


Mass: 22424.951 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#38: Protein/peptide 50S ribosomal protein uL5 /


Mass: 20177.564 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#39: Protein/peptide 50S ribosomal protein uL6 /


Mass: 19543.389 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#40: Protein/peptide 50S ribosomal protein uL10 /


Mass: 18101.748 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42923
#41: Protein/peptide 50S ribosomal protein uL11 /


Mass: 14951.442 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q06796
#42: Protein/peptide 50S ribosomal protein uL13 /


Mass: 16407.104 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#43: Protein/peptide 50S ribosomal protein uL14 /


Mass: 13175.288 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#44: Protein/peptide 50S ribosomal protein uL15 /


Mass: 15410.694 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#45: Protein/peptide 50S ribosomal protein uL16 /


Mass: 16223.049 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#46: Protein/peptide 50S ribosomal protein bL17 /


Mass: 13774.806 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#47: Protein/peptide 50S ribosomal protein uL18 /


Mass: 12993.829 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#48: Protein/peptide 50S ribosomal protein bL19 /


Mass: 13416.853 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#49: Protein/peptide 50S ribosomal protein bL20 /


Mass: 13669.189 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#50: Protein/peptide 50S ribosomal protein bL21 /


Mass: 11296.081 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#51: Protein/peptide 50S ribosomal protein uL22 /


Mass: 12481.608 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#52: Protein/peptide 50S ribosomal protein uL23 /


Mass: 10978.813 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#53: Protein/peptide 50S ribosomal protein uL24 /


Mass: 11166.120 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#54: Protein/peptide 50S ribosomal protein bL27 /


Mass: 10391.855 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657

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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
IDNameTypeParent ID
1B. subtilis MifM-stalled ribosome complexRIBOSOME0
270S ribosomeRIBOSOME1
3Membrane protein insertion and folding monitor1
4tRNA-Asp1
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 2 nm pre-coated Quantifoil R3/3 holey carbon support grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Apr 12, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 125085 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: defocus groups
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 305045 / Nominal pixel size: 1.108 / Actual pixel size: 1.108
Details: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, a FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012). (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Number of atoms included #LASTProtein: 35090 / Nucleic acid: 100335 / Ligand: 0 / Solvent: 0 / Total: 135425

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