EMD-8652

Single-particle
4.0 Å
EMD-8652
3D View Gallery
Deposition: 24/03/2017
Map released: 03/05/2017
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8652
Download
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)
Map and PDB model 5va3 summary report (pdf.gz) Map and 5va3 FULL report (pdf.gz)
EMICSS annotations (xml)

Cryo-EM structure of the human ether-a-go-go related K+ channel

EMD-8652

Single-particle
4.0 Å
EMD-8652
3D View Gallery
Deposition: 24/03/2017
Map released: 03/05/2017
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 6 mg/mL
Details: A 1 mL peak fraction was collected and concentrated ~3x to obtain the final ~6 mg/mL sample.
Buffer
pH: 7.4
Buffer components [7]:
Name Formula Concentration ChEBI
HEPES C8H18N2O4S 20.0 mM
Potassium chloride KCl 300.0 mM
Dithiothreitol C4H10O2S2 10.0 mM
N-Dodecyl beta-D-maltoside C24H46O11 0.025 %
Cholesteryl hemisuccinate C31H50O4 0.005 %
POPE:POPC:POPA 5:5:1 - 0.025 mg/mL -
Tris(2-carboxyethyl)phosphine C9H15O6P 0.5 mM
Details: PH 7.4, adjusted with NaOH
Grid
Mesh: 400
Model: Quantifoil R1.2/1.3
Material: GOLD
Pretreatment
Type: PLASMA CLEANING
Time: {'units': 's', 'valueOf_': '12'}
Atmosphere: AIR
Pressure: 101.325 kPa
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 98%
Chamber temperature: 298 K
Instrument: FEI VITROBOT MARK IV
Details: One blot: 3 second blot time, 0 blot force.
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 0.8 µm - 3.5 µm
Calibrated magnification: 38461.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 7420 pixel x 7676 pixel
Frames per image: 1-50
Number of grids: 1
Number of real images: 1505
Average exposure time: 15.0 s
Average electron dose per image: 85.0 e/Å2
Details: 50 0.3-second frames were collected for each movie at a dose rate of ~1.8 e-/A2/frame
Image processing [1]
Final reconstruction
Resolution: 4.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 4
Number of images used: 206
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C4
Software [1]
Name Version Details
FREALIGN 9.11 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: HERGTs map was used as initial model
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
FREALIGN 9.11 -
Particle selection [1]
Selected Ref. model Method Software Details
333000 - - - ~333k particles from autopick
Final 3D classification
Number of classes: 8
Avg. number of members per classes: 41625.0
Software [1]
Name Version Details
RELION 1.4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Human ether-a-go-go related K+ channel
⬡ Geometry
X Y Z
Dimensions 256 256 256
Origin 0 0 0
Spacing 256 256 256
Voxel size 0.56563 Å 0.56563 Å 0.46445 Å
Contour list
Primary Level Source
True 1.5 AUTHOR