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- EMDB-39463: 2.6A b-Galactosidase Structure Solved Using an Indirect Scintilla... -

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Basic information

Entry
Database: EMDB / ID: EMD-39463
Title2.6A b-Galactosidase Structure Solved Using an Indirect Scintillator-Coupled CMOS Detector at 300 kV
Map dataFSC-weighted, sharpend and masked map by PostProcess
Sample
  • Complex: beta-galactosidase
Keywordsb-galactosidase / CARBOHYDRATE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsAramaki S / Yoshida Y / Tanihara T / Oyama K / Otsuki K / Terada Y / Matsunaga N / Ohdo S / Mayanagi K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: High-Resolution Single Particle Analysis Using an Indirect Scintillator-Coupled CMOS Detector at 300 kV
Authors: Aramaki S / Yoshida Y / Tanihara T / Oyama K / Otsuki K / Terada Y / Matsunaga N / Ohdo S / Mayanagi K
History
DepositionMar 16, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39463.png

Downloads & links

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Map

FileDownload / File: emd_39463.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFSC-weighted, sharpend and masked map by PostProcess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 221.44 Å		0.87 Å/pix.
x 256 pix.
= 221.44 Å		0.87 Å/pix.
x 256 pix.
= 221.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.865 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.051121973 - 0.106416106
Average (Standard dev.)0.00040896298 (±0.004895964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 221.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39463_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39463_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_39463_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 : beta-galactosidase

EntireName: beta-galactosidase
Components
  • Complex: beta-galactosidase

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Supramolecule #1: beta-galactosidase

SupramoleculeName: beta-galactosidase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 465 KDa

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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

Concentration2.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris HCl
50.0 mMNaClsodium chloride
1.0 mMC4H10O2S2DTT
2.0 mMMgCl2magnesium chloride
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: GloQube Plus
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9603 / Average exposure time: 2.3 sec. / Average electron dose: 107.0 e/Å2 / Details: TVIPS TemCam-XF416 (4k x 4k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 200000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 622690
Startup modelType of model: NONE / Details: from 3D initial reference process in RELION
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Number images used: 386962
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
FSC plot (resolution estimation)

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