EMD-4584

Subtomogram averaging
20.4 Å
EMD-4584
3D View Gallery
Deposition: 01/02/2019
Map released: 14/08/2019
Last modified: 25/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-4584
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
EMICSS annotations (xml)

Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1

EMD-4584

Subtomogram averaging
20.4 Å
EMD-4584
3D View Gallery
Deposition: 01/02/2019
Map released: 14/08/2019
Last modified: 25/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Concentration: 5 mg/mL
Details: Sample was prepared in the described buffer. Just before freezing 6 nm colloidal gold fiducial marker were added to the sample in a 1:1 ratio.
Buffer
pH: 7.4
Details: 20 mM HEPES, 200 mM NaCl, residual MgCl2, 9mM KCl.
Grid
Model: Quantifoil R2/2
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 70%
Chamber temperature: 277.15 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 2.0 µm - 4.0 µm
Nominal magnification: 53000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Specialist optics
Energy filter
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Average electron dose per image: 2.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 20.4 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
Dynamo 1.1.266 -
⦩ Final angle assignment
Type: OTHER
Details: Subtomogram averaging by cross correlation maximization
Software [1]
Name Version Details
Dynamo 1.1.266 Independent half-set refinement
Final 3D classification
Number of classes: 1
Avg. number of members per classes: 1677.0
Software [1]
Name Version Details
Dynamo 1.1.266 -
Extraction
Number of images used: 2214
Reference model: Global average of the particles rotated to the known initial orientations
Method: Geometry-assisted particle picking form tube surfaces
Software [1]
Name Version Details
Dynamo 1.1.266 -
CTF correction
Details:CTF determination was done by Gctf and correction was performed by ctfphaseflip from IMOD
Software [2]
Name Version Details
Gctf 1.06 Detection
IMOD 4.10 Correction
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: None
⬡ Geometry
X Y Z
Dimensions 280 280 280
Origin 0 0 0
Spacing 280 280 280
Voxel size 2.7 Å 2.7 Å 2.7 Å
Contour list
Primary Level Source
True 1.0 AUTHOR