EMD-7788

Single-particle
4.93 Å
EMD-7788
3D View Gallery
Deposition: 15/04/2018
Map released: 23/05/2018
Last modified: 10/10/2018
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Overview 3D View Sample Experiment Validation Additional data Links

EMD-7788
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EMICSS annotations (xml)

Insulin Receptor ectodomain in complex with two insulin molecules plunged with a spot-to-plunge time of 200 ms

EMD-7788

Single-particle
4.93 Å
EMD-7788
3D View Gallery
Deposition: 15/04/2018
Map released: 23/05/2018
Last modified: 10/10/2018
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.5
Grid
Model: Homemade
Vitrification
Cryogen name: ETHANE
Instrument: OTHER
Details: 200 ms spot-to-plunge time. The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK I', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file.
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: 0.01 mm
Nominal magnification: 105000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Specialist optics
SPH aberration_corrector: Corrected so that Cs is as close to 0 as possible.
Energy filter
Name: GIF Bioquantum
Image Recording [1]
Detector model: GATAN K2 QUANTUM (4k x 4k)
Detector mode: COUNTING
Average exposure time: 10.0 s
Average electron dose per image: 66.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 4.93 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 40390
⌯ Applied Symmetry
Point group: C2
Software [1]
Name Version Details
CryoSPARC 0.6.5 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: CryoSPARC ab-initio
⦨ Initial angle assignment
Type: OTHER
Details: CryoSPARC SGD
Software [1]
Name Version Details
CryoSPARC 0.6.5 -
⦩ Final angle assignment
Type: OTHER
Details: CryoSPARC SGD
Software [1]
Name Version Details
CryoSPARC 0.6.5 -
Particle selection [1]
Selected Ref. model Method Software Details
83513 - - - -
Final 3D classification
Details: The best-looking class was used for full refinement.
Software [1]
Name Version Details
CryoSPARC 0.6.5 -
CTF correction
Software [1]
Name Version Details
Gctf - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: CryoSPARC auto-generated sharpened full map from the last iteration of independent refinement.
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 288 288 288
Dimensions (Å) 316.80002 316.80002 316.80002
Voxel size (Å) 1.1 1.1 1.1
Contour list
Primary Level Source
True 0.614 AUTHOR