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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: J Struct Biol / Year: 2026
Title: High-Resolution single particle analysis using a scintillator camera XF416 on CRYOARM300II at 300 kV.
Authors: Shinji Aramaki / Tomohito Tanihara / Yuya Yoshida / Naoya Matsunaga / Shigehiro Ohdo / Kouta Mayanagi /
Abstract: The advent of direct electron detectors (DEDs) has driven a major breakthrough in cryo-electron microscopy (cryo-EM), particularly in single-particle analysis (SPA), establishing DEDs as essential ...The advent of direct electron detectors (DEDs) has driven a major breakthrough in cryo-electron microscopy (cryo-EM), particularly in single-particle analysis (SPA), establishing DEDs as essential tools for achieving near-atomic resolution. In this study, we re-evaluated the performance of the TVIPS TemCam-XF416, an indirect scintillator-coupled CMOS camera (scintillator camera). Using a JEOL CRYOARM 300II, we performed SPA on two well-established benchmark specimens, β-galactosidase and apoferritin, at a 300 kV acceleration voltage. The resulting reconstructions reached resolutions of 2.6 Å and 2.1 Å, respectively. Notably, the apoferritin map clearly resolves the central holes of aromatic side chains-a level of detail previously considered exclusive to DEDs. These results were achieved by implementing the latest standard reconstruction workflows, including motion correction and contrast transfer function refinement, underscoring the critical role of computational methods in attaining high-resolution structures. While scintillator cameras inherently exhibit a lower signal-to-noise ratio than DEDs, our findings with XF416 demonstrate that, with appropriate data collection and processing, such cameras can deliver near-atomic resolution structures. This work establishes a crucial technical benchmark for the scintillator camera evaluated in this study on a high-end 300 kV cryo-EM platform, demonstrating its capability to achieve resolutions suitable for many structural biology applications and providing an updated perspective on its performance capabilities.
History
DepositionMar 16, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing 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
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.865 Å
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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
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Half map: #1

Fileemd_39463_half_map_1.map
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Half map: #2

Fileemd_39463_half_map_2.map
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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
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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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