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- PDB-9i5t: 50S subunit of P. gingivalis ribosome with Lefamulin -

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Basic information

Entry
Database: PDB / ID: 9i5t
Title50S subunit of P. gingivalis ribosome with Lefamulin
Components
  • (Large ribosomal subunit protein ...) x 29
  • 23S rRNA
  • 5S rRNA
  • DUF4295 domain-containing protein
KeywordsRIBOSOME / antibiotics / macrolide-resistance
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 signature. / Ribosomal protein L31 ...Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / :
Similarity search - Domain/homology
Lefamulin / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / DUF4295 domain-containing protein / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 ...Lefamulin / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / DUF4295 domain-containing protein / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHiregange, D.G. / Bashan, A. / Yonath, A.
Funding support1items
OrganizationGrant numberCountry
Other privateTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor ...Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor Kaczmarczyk / Aneta Sroka / Masato Taoka / Yuko Nobe / Toshiaki Isobe / Susanne Paukner / Ella Zimmerman / Anat Bashan / Jan Potempa / Ada Yonath /
Abstract: Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its ...Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its propensity to form biofilms pose a challenge to effective treatment. To explore therapeutic avenues, we studied the high-resolution cryogenic electron microscope structures of ribosomes from the wild-type P. gingivalis W83 and the macrolide-resistant mutant strain ermΔporN. The structural analysis revealed unique features primarily at the ribosome periphery. Together with the distinctive distribution of ribosomal RNA modifications, these findings offer insights into the therapeutical potential, such as creation of novel therapeutic compounds inhibiting the specific cellular functions of the P. gingivalis ribosomes. Moreover, the high-resolution structure of the ermΔporN ribosome in its complex with the approved antibiotic lefamulin suggests its repurposing against P. gingivalis. Furthermore, we provide a foundation for additional effective strategies to treat periodontitis and associated systemic diseases.
History
DepositionJan 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Large ribosomal subunit protein bL28
1: Large ribosomal subunit protein uL29
11: Large ribosomal subunit protein uL5
12: Large ribosomal subunit protein bL31B
2: Large ribosomal subunit protein uL30
4: Large ribosomal subunit protein bL32
6: Large ribosomal subunit protein bL34
7: Large ribosomal subunit protein bL35
8: Large ribosomal subunit protein bL36
A: 23S rRNA
B: 5S rRNA
D: Large ribosomal subunit protein uL2
E: Large ribosomal subunit protein uL3
F: Large ribosomal subunit protein uL4
M: Large ribosomal subunit protein uL13
O: Large ribosomal subunit protein uL15
P: Large ribosomal subunit protein uL16
Q: Large ribosomal subunit protein bL17
R: Large ribosomal subunit protein uL18
S: Large ribosomal subunit protein bL19
T: Large ribosomal subunit protein bL20
U: Large ribosomal subunit protein bL21
V: Large ribosomal subunit protein uL22
W: Large ribosomal subunit protein uL23
X: Large ribosomal subunit protein uL24
Y: Large ribosomal subunit protein bL25
Z: Large ribosomal subunit protein bL27
h: Large ribosomal subunit protein bL9
15: DUF4295 domain-containing protein
13: Large ribosomal subunit protein uL6
N: Large ribosomal subunit protein uL14
5: Large ribosomal subunit protein bL33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,381,236206
Polymers1,376,23632
Non-polymers5,000174
Water24,8611380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Large ribosomal subunit protein ... , 29 types, 29 molecules 01111224678DEFMOPQRSTUVWXYZh13N5

#1: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9027.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RM15
#2: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7499.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY4
#3: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20912.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY0
#4: Protein Large ribosomal subunit protein bL31B / 50S ribosomal protein L31 type B


Mass: 9816.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIG0
#5: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6700.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLX4
#6: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6958.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RH62
#7: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5761.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIL8
#8: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7518.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RJD8
#9: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4601.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLW9
#12: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29778.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY9
#13: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 21925.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLZ2
#14: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 23247.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTL4
#15: Protein Large ribosomal subunit protein uL13


Mass: 17075.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MX43
#16: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15616.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTN2
#17: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 16344.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY5
#18: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 18074.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLW4
#19: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12560.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTM9
#20: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 14120.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RGQ9
#21: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13324.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MVQ8
#22: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11843.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MX95
#23: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 15357.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY7
#24: Protein Large ribosomal subunit protein uL23


Mass: 11116.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: A0A134DR82
#25: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11627.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY1
#26: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25 / General stress protein CTC


Mass: 21028.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RHF3
#27: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9244.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLC1
#28: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 19356.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIG5
#30: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 20389.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLX7
#31: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13086.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY2
#32: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 7356.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RM14

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RNA chain , 2 types, 2 molecules AB

#10: RNA chain 23S rRNA


Mass: 934217.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)
#11: RNA chain 5S rRNA


Mass: 35186.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)

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Protein/peptide , 1 types, 1 molecules 15

#29: Protein/peptide DUF4295 domain-containing protein


Mass: 5559.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: A0AAE9XCN0

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Non-polymers , 6 types, 1554 molecules

#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 139 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#35: Chemical ChemComp-62B / Lefamulin


Mass: 507.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H45NO5S / Comment: medication, antibiotic*YM
#36: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#37: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1380 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 50S subunit of P. gingivalis ribosome with Lefamulin / Type: RIBOSOME / Entity ID: #1-#10, #12-#32 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223396 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00687897
ELECTRON MICROSCOPYf_angle_d0.77131796
ELECTRON MICROSCOPYf_dihedral_angle_d14.35534971
ELECTRON MICROSCOPYf_chiral_restr0.0417009
ELECTRON MICROSCOPYf_plane_restr0.0076884

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