EMD-22009

Single-particle
3.0 Å
EMD-22009
3D View Gallery
Deposition: 20/05/2020
Map released: 18/11/2020
Last modified: 06/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-22009
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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)
Map and PDB model 6x2j summary report (pdf.gz) Map and 6x2j FULL report (pdf.gz)
EMICSS annotations (xml)

Structure of human TRPA1 in complex with agonist GNE551

EMD-22009

Single-particle
3.0 Å
EMD-22009
3D View Gallery
Deposition: 20/05/2020
Map released: 18/11/2020
Last modified: 06/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.33 mg/mL
Buffer
pH: 8.2
Buffer components [3]:
Name Formula Concentration ChEBI
Tris - 25.0 mM -
NaCl NaCl 150.0 mM
TCEP - 0.5 mM -
Grid
Mesh: 300
Model: Quantifoil R0.6/1
Material: GOLD
Details: Solarus plasma cleaner
Pretreatment
Type: PLASMA CLEANING
Time: {'units': 's', 'valueOf_': '30'}
Atmosphere: OTHER
Pressure: 0.1 kPa
Support Film [2]
Material Topology Thickness
CARBON HOLEY -
GOLD HOLEY 25.0
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Details: Triple blot. Put blot in vitroblot Apply 3.5ul to grid, wait 30sec, blot manually Apply 3.5ul to grid, wait 30sec, blot manually, apply final 3.5ul, final blot by vitrobot (3.5s).
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 magnification: 165000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Specialist optics
Energy filter
Name: GIF Bioquantum
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 QUANTUM (4k x 4k)
Detector mode: COUNTING
Frames per image: 1-40
Number of grids: 1
Number of real images: 11063
Average exposure time: 1.6 s
Average electron dose per image: 41.8 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 58837
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C4
Software [1]
Name Version Details
CisTEM - -
Startup model [1]
Type: NONE
⦨ Initial angle assignment
Type: RANDOM ASSIGNMENT
Software [1]
Name Version Details
CisTEM - -
⦩ Final angle assignment
Type: OTHER
Software [1]
Name Version Details
CisTEM - -
Particle selection [1]
Selected Ref. model Method Software Details
505112 - - - -
Final 3D classification
Number of classes: 5
Software [2]
Name Version Details
CisTEM - 3D reconstruction
PHENIX - Density modification
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Density-modified map
⬡ Geometry
X Y Z
Dimensions 324 324 324
Origin 0 0 0
Spacing 324 324 324
Voxel size 1.0 Å 1.0 Å 1.0 Å
Contour list
Primary Level Source
True 0.2 AUTHOR