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- EMDB-44578: iSAT PNA - RB0811-C-b1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44578
TitleiSAT PNA - RB0811-C-b1
Map dataAligned and rescaled to reference 4YBB 50S model
Sample
  • Complex: iSAT control - ctrl-C-a1 50S ribosomal subunit assembly intermediate
KeywordsRibosome / 50S intermediate / RNP
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsSheng K / Dong X / Williamson JR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-136412 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI170855 United States
CitationJournal: To Be Published
Title: Augmenting the Bacterial Ribosome Assembly Structurome using Anti-Sense Oligonucleotide Analogs
Authors: Sheng K / Dong X / Aiyer S / Lee J / Marquardt S / Lyumkis D / Wiliamson JR
History
DepositionApr 23, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44578.png

Downloads & links

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Map

FileDownload / File: emd_44578.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAligned and rescaled to reference 4YBB 50S model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 160 pix.
= 419.2 Å		2.62 Å/pix.
x 160 pix.
= 419.2 Å		2.62 Å/pix.
x 160 pix.
= 419.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.3926155 - 1.220196
Average (Standard dev.)-0.00037114028 (±0.077723645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 419.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44578_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44578_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : iSAT control - ctrl-C-a1 50S ribosomal subunit assembly intermediate

EntireName: iSAT control - ctrl-C-a1 50S ribosomal subunit assembly intermediate
Components
  • Complex: iSAT control - ctrl-C-a1 50S ribosomal subunit assembly intermediate

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Supramolecule #1: iSAT control - ctrl-C-a1 50S ribosomal subunit assembly intermediate

SupramoleculeName: iSAT control - ctrl-C-a1 50S ribosomal subunit assembly intermediate
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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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

BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
100.0 mMammonium chlorideNH4Cl
10.0 mMmagnesium chlorideMgCl2
0.5 mMEDTA
6.0 mMbeta-mercaptoethanol
VitrificationCryogen name: ETHANE / Chamber humidity: 80 %
Details0.1 uM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 36.71 e/Å2 / Details: data were collected with tilts at 30 degree
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Best FSC was chosen in CryoSPARC / Number images used: 1457
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-Uniform refinement in CryoSPARC was used.
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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