EMD-7987

Single-particle
4.47 Å
EMD-7987
3D View Gallery
Deposition: 11/06/2018
Map released: 01/08/2018
Last modified: 20/11/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-7987
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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 6dr0 summary report (pdf.gz) Map and 6dr0 FULL report (pdf.gz)
EMICSS annotations (xml)

Class 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor

EMD-7987

Single-particle
4.47 Å
EMD-7987
3D View Gallery
Deposition: 11/06/2018
Map released: 01/08/2018
Last modified: 20/11/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 8 mg/mL
Details: Type 3 inositol 1,4,5-trisphosphate receptor in detergent micelles
Buffer
pH: 8.0
Buffer components [6]:
Name Formula Concentration ChEBI
Sodium Chlorid NaCl 150.0 mM
Tris(hydroxymethyl)aminomethane hydrochloride Tris 50.0 mM
1,4-Dithiothreitol DTT 2.0 mM
Digitonin Digitonin 0.06 percent
Ethylene glycol-bis(aminoethyl ether)-N,N,N',N'-tetraacetic acid EGTA 5.0 mM
Inositol triphosphate IP3 50.0 micromolar
Details: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA 50 micromolar IP3
Grid
Mesh: 400
Model: Quantifoil R1.2/1.3
Material: GOLD
Support Film [1]
Material Topology Thickness
CARBON HOLEY ARRAY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 293 K
Instrument: FEI VITROBOT MARK IV
Details: Blot for 2 seconds prior to freezing.
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: 1.0 µm -
Nominal magnification: 22500.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 7420 pixel x 7676 pixel
Frames per image: 1-40
Number of grids: 1
Number of real images: 4519
Average exposure time: 8.0 s
Average electron dose per image: 61.0 e/Å2
Image processing [1]
Details: Movie frames were aligned with MotionCor2
Final reconstruction
Resolution: 4.47 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 27334
Algorithm: FOURIER SPACE
Details:
Software [1]
Name Version Details
FREALIGN - -
Startup model [1]
Type: OTHER
Details:CryoSPARC initial model
⦨ Initial angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
FREALIGN - -
⦩ Final angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
FREALIGN - -
Particle selection [1]
Selected Ref. model Method Software Details
302966 - - - -
Final 3D classification
Number of classes: 7
Avg. number of members per classes: 43281.0
Software [1]
Name Version Details
RELION - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Class 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 384 384 384
Dimensions (Å) 417.79202 417.79202 417.79202
Voxel size (Å) 1.088 1.088 1.088
Contour list
Primary Level Source
True 3.06 AUTHOR