EMD-5778

Single-particle
3.275 Å
EMD-5778
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Deposition: 24/10/2013
Map released: 04/12/2013
Last modified: 14/10/2015
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EMD-5778
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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)
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EMICSS annotations (xml)

Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy

EMD-5778

Single-particle
3.275 Å
EMD-5778
3D View Gallery
Deposition: 24/10/2013
Map released: 04/12/2013
Last modified: 14/10/2015
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.3 mg/mL
Buffer
pH: 7.4
Details: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP
Grid
Details: 400 mesh Quantifoil grid
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 120 K
Instrument: FEI VITROBOT MARK III
Method: Blot for 6 sec
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.0 mm
Nominal defocus: 1.5 µm - 3.0 µm
Nominal magnification: 31000.0
Calibrated magnification: 31000.0
Specimen holder model: OTHER
Specimen holder details: Cooled to Liquid Nitrogen temperature
Details: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
Image Recording [1]
Detector category: CCD
Detector model: GATAN K2 (4k x 4k)
Number of real images: 946
Average electron dose per image: 21 e/Å2
Details: Every image is the average of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images averaged from frames #3-#16.
Image processing [1]
Details: 3D classification, refinement, and reconstruction were performed using RELION.
Final reconstruction
Resolution: 3.275 Å ( BY AUTHOR)
Resolution method: OTHER
Number of images used: 35645
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group: C4
Software [1]
Name Version Details
RELION - -
CTF correction
Details:Each particle
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Structure of the capsaicin receptor, TRPV1. This map is direct output from RELION without sharpening using a negative temperature factor. The map was normalized using the program MAPMAN.
Details: ::::EMDATABANK.org::::EMD-5778::::
⬡ Geometry
X Y Z
Dimensions 256 256 256
Origin -128 -128 -128
Spacing 256 256 256
Voxel size 1.2156 Å 1.2156 Å 1.2156 Å
Contour list
Primary Level Source
True 7.0 AUTHOR