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- EMDB-9203: bovine glutamate dehydrogenase (18apr21a) -

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Basic information

Entry
Database: EMDB / ID: EMD-9203
Titlebovine glutamate dehydrogenase (18apr21a)
Map databovine glutamate dehydrogenase map (18apr21a)
Sample
  • Complex: bovine liver glutamate dehydrogenase
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsEng ET / Kopylov M / Negro CJ / Dallaykan S / Jordan KJ / Kelley K / Rice WJ / Carragher BO / Potter CS
CitationJournal: J Struct Biol / Year: 2019
Title: Reducing cryoEM file storage using lossy image formats.
Authors: Edward T Eng / Mykhailo Kopylov / Carl J Negro / Sarkis Dallaykan / William J Rice / Kelsey D Jordan / Kotaro Kelley / Bridget Carragher / Clinton S Potter /
Abstract: Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. High levels of automation and faster data acquisition rates require hard ...Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. High levels of automation and faster data acquisition rates require hard decisions to be made regarding data retention. Here we investigate the efficacy of data compression applied to aligned summed movie files. Surprisingly, these images can be compressed using a standard lossy method that reduces file storage by 90-95% and yet can still be processed to provide sub-2 Å reconstructed maps. We do not advocate this as an archival method, but it may provide a useful means for retaining images as an historical record, especially at large facilities.
History
DepositionOct 13, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseOct 24, 2018-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9203.png

Downloads & links

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Map

FileDownload / File: emd_9203.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbovine glutamate dehydrogenase map (18apr21a)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 352 pix.
= 232.883 Å		0.66 Å/pix.
x 352 pix.
= 232.883 Å		0.66 Å/pix.
x 352 pix.
= 232.883 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6616 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07137104 - 0.14005539
Average (Standard dev.)0.00017214128 (±0.0037602698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 232.8832 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.661599431818180.661599431818180.66159943181818
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z232.883232.883232.883
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0710.1400.000

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Supplemental data

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Mask #1

Fileemd_9203_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_9203_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: odd half map

Fileemd_9203_half_map_1.map
Annotationodd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even half map

Fileemd_9203_half_map_2.map
Annotationeven half 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 : bovine liver glutamate dehydrogenase

EntireName: bovine liver glutamate dehydrogenase
Components
  • Complex: bovine liver glutamate dehydrogenase

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Supramolecule #1: bovine liver glutamate dehydrogenase

SupramoleculeName: bovine liver glutamate dehydrogenase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 347 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

Concentration4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Blotted for 2.5 s after a 30 s wait time.
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
DetailsLeginon
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 2491 / Average exposure time: 10.2083 sec. / Average electron dose: 61.25 e/Å2
Details: Images were collected in movie mode at 10 frames per second.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.02 µm / Calibrated defocus min: 0.2 µm / Calibrated magnification: 75574 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000
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

DetailsImages were automatically run through MotionCor2 by Appion on-the-fly with the aligned sum and aligned dose-weighted sum saved.
Particle selectionNumber selected: 583375
Details: Template picking by FindEM. Templates were created by Appion DoG picks from the first 50 images, which were subjected to 2D classification in RELION.
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Details: CTF amplitude correction was performed following 3D reconstruction.
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model created by cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 285518
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3)
Details: 3D classification used K=3 and 1 out of the 3 classes were chosen for the final refinement.
FSC plot (resolution estimation)

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