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- PDB-9q40: Pseudomonas aeruginosa 50S ribosome bound to RsfS (L1 stalk in 'm... -

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Basic information

Entry
Database: PDB / ID: 9q40
TitlePseudomonas aeruginosa 50S ribosome bound to RsfS (L1 stalk in 'mid' conformation)
Components
  • (Large ribosomal subunit protein ...) x 31
  • 23S rRNA
  • 5S rRNA
  • Ribosomal silencing factor RsfS
  • tRNA-Ala
KeywordsRIBOSOME / 50S Ribosome / ribosome silencing factor during starvation / RsfS / Pseudomonas aeruginosa
Function / homology
Function and homology information


negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / assembly of large subunit precursor of preribosome / regulation of translation / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding ...negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / assembly of large subunit precursor of preribosome / regulation of translation / transferase activity / ribosome binding / 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 / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein uL10 C-terminal region / Ribosomal protein L1, bacterial-type / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal ...Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein uL10 C-terminal region / Ribosomal protein L1, bacterial-type / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L20 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL33 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36A / Ribosomal silencing factor RsfS / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsFindlay, J.L. / Kanik, M. / Gauvin, C.C. / Franklin, M.J. / Lawrence, C.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH 1R41GM148117 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R41GM153173 United States
National Science Foundation (NSF, United States)NSF DBI-1828765 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH P30GM140963 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R21 AI154171 United States
CitationJournal: To Be Published
Title: RsfS Prevents 70S Formation During Active Cell Growth in P. aeruginosa
Authors: Findlay, J.L. / Kanik, M. / Franklin, M.J. / Lawrence, C.M.
History
DepositionAug 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
C: Large ribosomal subunit protein uL1
D: Large ribosomal subunit protein uL2
E: Large ribosomal subunit protein uL3
F: Large ribosomal subunit protein uL4
G: Large ribosomal subunit protein uL5
H: Large ribosomal subunit protein uL6
I: Large ribosomal subunit protein bL9
L: Large ribosomal subunit protein uL13
M: Large ribosomal subunit protein uL14
N: Large ribosomal subunit protein uL15
O: Large ribosomal subunit protein uL16
P: Large ribosomal subunit protein bL17
Q: Large ribosomal subunit protein uL18
R: Large ribosomal subunit protein bL19
S: Large ribosomal subunit protein bL20
T: Large ribosomal subunit protein bL21
U: Large ribosomal subunit protein uL22
V: Large ribosomal subunit protein uL23
W: Large ribosomal subunit protein uL24
X: Large ribosomal subunit protein bL25
Y: Large ribosomal subunit protein bL27
Z: Large ribosomal subunit protein bL28
1: Large ribosomal subunit protein uL29
2: Large ribosomal subunit protein uL30
4: Large ribosomal subunit protein bL32
5: Large ribosomal subunit protein bL33
6: Large ribosomal subunit protein bL34
7: Large ribosomal subunit protein bL35
8: Large ribosomal subunit protein bL36A
9: Ribosomal silencing factor RsfS
v: tRNA-Ala
J: Large ribosomal subunit protein uL10
K: Large ribosomal subunit protein uL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,448,389238
Polymers1,443,41435
Non-polymers4,975203
Water88,3284903
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules ABv

#1: RNA chain 23S rRNA


Mass: 937447.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 110227054
#2: RNA chain 5S rRNA


Mass: 38902.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: AE004091.2
#33: RNA chain tRNA-Ala


Mass: 24490.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: AE004091.2

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Large ribosomal subunit protein ... , 31 types, 31 molecules CDEFGHILMNOPQRSTUVWXYZ1245678JK

#3: Protein Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL1


Mass: 24267.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWC6
#4: Protein Large ribosomal subunit protein uL2


Mass: 29641.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD8
#5: Protein Large ribosomal subunit protein uL3


Mass: 22625.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD5
#6: Protein Large ribosomal subunit protein uL4


Mass: 21673.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD6
#7: Protein Large ribosomal subunit protein uL5


Mass: 20424.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE7
#8: Protein Large ribosomal subunit protein uL6


Mass: 19129.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF0
#9: Protein Large ribosomal subunit protein bL9


Mass: 15551.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUN2
#10: Protein Large ribosomal subunit protein uL13


Mass: 16058.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVY2
#11: Protein Large ribosomal subunit protein uL14


Mass: 13435.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE5
#12: Protein Large ribosomal subunit protein uL15


Mass: 15204.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF4
#13: Protein Large ribosomal subunit protein uL16


Mass: 15434.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE2
#14: Protein Large ribosomal subunit protein bL17


Mass: 14533.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O52761
#15: Protein Large ribosomal subunit protein uL18


Mass: 12687.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF1
#16: Protein Large ribosomal subunit protein bL19


Mass: 13055.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HXQ2
#17: Protein Large ribosomal subunit protein bL20


Mass: 13397.972 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I0A2
#18: Protein Large ribosomal subunit protein bL21


Mass: 11678.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVL6
#19: Protein Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL22


Mass: 11935.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE0
#20: Protein Large ribosomal subunit protein uL23


Mass: 10969.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD7
#21: Protein Large ribosomal subunit protein uL24


Mass: 11494.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE6
#22: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 21994.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVC4
#23: Protein Large ribosomal subunit protein bL27


Mass: 9010.450 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVL7
#24: Protein Large ribosomal subunit protein bL28


Mass: 9087.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HTN8
#25: Protein Large ribosomal subunit protein uL29


Mass: 7213.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE3
#26: Protein Large ribosomal subunit protein uL30


Mass: 6489.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF3
#27: Protein Large ribosomal subunit protein bL32


Mass: 6807.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HZN4
#28: Protein Large ribosomal subunit protein bL33


Mass: 6060.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HTN9
#29: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5226.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P29436
#30: Protein Large ribosomal subunit protein bL35


Mass: 7387.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I0A1
#31: Protein/peptide Large ribosomal subunit protein bL36A


Mass: 4447.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF6
#34: Protein Large ribosomal subunit protein uL10


Mass: 17657.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWC7
#35: Protein Large ribosomal subunit protein uL10


Mass: 14925.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWC5

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Protein , 1 types, 1 molecules 9

#32: Protein Ribosomal silencing factor RsfS


Mass: 13066.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HX22

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Non-polymers , 3 types, 5106 molecules

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


Mass: 24.305 Da / Num. of mol.: 202 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4903 / 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: Ribosome fraction isolated from wild type P. aeruginosa cells during exponential phase growth.
Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Molecular weightValue: 1.49 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCLC4H12ClNO31
2300 mMAmmonium ChlorideNH4Cl1
310.5 mMManesium acetateMg(CH3COO)21
40.5 mMEDTAC10H16N2O81
53 mMbeta-mercaptoethanolC2H6OS1
SpecimenConc.: 2.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: Blot time: 5 seconds Blot force: 3

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 54.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 13721 / Details: 50 frames per movie at 0.1 seconds per frame
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.1particle selection
2SerialEM4.1image acquisition
4cryoSPARCv4.7.1CTF correction
7Coot0.9.5model fitting
9PHENIX1.20.1_4487model refinement
10cryoSPARCv4.7.1initial Euler assignment
11cryoSPARCv4.7.1final Euler assignment
12cryoSPARCv4.7.1classification
13cryoSPARCv4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1665000
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 452165 / Algorithm: EXACT BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initially, each chain of the 7UNW 50S subunit was rigid body fit into the experimental map. Occasionally Alpha fold 2 generated models of individual chains were used instead. Models were then refined in phenix.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17UNW

7unw

17UNW1PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 2.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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