EMD-7041

Single-particle
3.7 Å
EMD-7041
3D View Gallery
Deposition: 22/09/2017
Map released: 22/11/2017
Last modified: 13/11/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-7041
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

Cryo-EM structure of human insulin degrading enzyme in complex with insulin

EMD-7041

Single-particle
3.7 Å
EMD-7041
3D View Gallery
Deposition: 22/09/2017
Map released: 22/11/2017
Last modified: 13/11/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.3 mg/mL
Details: The sample was monodisperse
Buffer
pH: 7.8
Buffer components [3]:
Name Formula Concentration ChEBI
HEPES C8H18N2O4S 20.0 mmol/L
Sodium chloride NaCl 300.0 mmol/L
EDTA C10H16N2O8 20.0 mmol/L
Grid
Mesh: 300
Model: Homemade nanowire grid
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Time: 10 s
Atmosphere: OTHER
Pressure: 0.001 kPa
Support Film [1]
Material Topology Thickness
CARBON HOLEY 10.0
Vitrification
Cryogen name: ETHANE
Chamber humidity: 85%
Chamber temperature: 298 K
Instrument: HOMEMADE PLUNGER
Details: The cryo grids were made using Spotiton and homemade plunger.
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: 0.9400000000000001 µm - 2.2 µm
Nominal magnification: 22500.0
Calibrated magnification: 46598.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE ( Residual tilt: 10.0 mrad)
Temperature
Minimum: 70.0 K
Maximum: 70.0 K
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3710 pixel x 3838 pixel
Frames per image: 1-50
Number of grids: 3
Number of real images: 3085
Average exposure time: 10.0 s
Average electron dose per image: 71.4 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.7 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 116122
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: PDB ENTRY
PDB model: 3QZ2
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Number of reference projections: 2
Software [1]
Name Version Details
RELION 2.0 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Number of reference projections: 2
Software [1]
Name Version Details
RELION 2.0 -
Particle selection [1]
Selected Ref. model Method Software Details
762283 - - - -
Final 3D classification
Number of classes: 8
Avg. number of members per classes: 18549.0
Software [1]
Name Version Details
RELION 2.0 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: This is the sharpened map from the final, Insulin degrading enzyme in complex with insulin
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 320 320 320
Dimensions (Å) 343.36 343.36 343.36
Voxel size (Å) 1.073 1.073 1.073
Contour list
Primary Level Source
True 0.053 AUTHOR