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- EMDB-7562: Rabbit muscle aldolase at 3.5 A resolution (17nov02c less 25nm ic... -

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Basic information

Entry
Database: EMDB / ID: 7562
TitleRabbit muscle aldolase at 3.5 A resolution (17nov02c less 25nm ice thickness, 22k particles)
Map datarabbit muscle aldolase at 3.5 A resolution (17nov02c <25nm ice thickness, 22k particles)
SampleRabbit muscle aldolase at 3.5 A resolution (17nov02c <25 nm ice thickness, 22k particles):
Rabbit muscle aldolase
SourceOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsKim LK / Rice WJ / Eng ET / Kopylov M / Cheng A / Raczkowski AM / Jordan KD / Bobe D / Potter CS / Carragher B
CitationJournal: Front Mol Biosci / Year: 2018
Title: Benchmarking cryo-EM Single Particle Analysis Workflow.
Authors: Laura Y Kim / William J Rice / Edward T Eng / Mykhailo Kopylov / Anchi Cheng / Ashleigh M Raczkowski / Kelsey D Jordan / Daija Bobe / Clinton S Potter / Bridget Carragher
DateDeposition: Mar 16, 2018 / Header (metadata) release: Apr 18, 2018 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.349
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.349
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7562.png

Downloads & links

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Map

Fileemd_7562.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
0.86 Å/pix.
= 218.88 Å		256 pix
0.86 Å/pix.
= 218.88 Å		256 pix
0.86 Å/pix.
= 218.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.349 (by author), 0.349 (movie #1):
Minimum - Maximum-0.595059 - 1.4632977
Average (Standard dev.)0.00001197314 (0.050325908)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 218.88 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z218.880218.880218.880
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5951.4630.000

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Supplemental data

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Sample components

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Entire Rabbit muscle aldolase at 3.5 A resolution (17nov02c <25 nm ice t...

EntireName: Rabbit muscle aldolase at 3.5 A resolution (17nov02c <25 nm ice thickness, 22k particles) / Number of components: 2

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Component #1: protein, Rabbit muscle aldolase at 3.5 A resolution (17nov02c <25...

ProteinName: Rabbit muscle aldolase at 3.5 A resolution (17nov02c <25 nm ice thickness, 22k particles) / Recombinant expression: No
MassExperimental: 150 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Rabbit muscle aldolase

ProteinName: Rabbit muscle aldolase / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 65 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Raw dataEMPIAR-10183 (Title: Benchmarking cryo-EM single particle analysis workflow
Data size: 345.0
Data #1: aligned micrographs of rabbit muscle aldolase 17nov02c [micrographs - multiframe])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 22000
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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