EMD-20215 Experiments and Validation

CRYO-EM STRUCTURE OF PHOSPHORYLATED AP-2 CORE BOUND TO NECAP

Single particle reconstruction
Overview of EMD-20215
Sample name: PHOSPHORYLATED AP2-NECAP CO-COMPLEX
Organisms: Mus musculus, Rattus norvegicus
Fitted atomic model: 6owo
Related EM entry by publication: EMD-20220

Map parameters

Recommended contour level: 0.03 (author)
Number of grid points: 300 × 300 × 300
Voxel size: 1.16 × 1.16 × 1.16 Å
Minimum density: -0.091
Maximum density: 0.175
Average density: 0.00
Standard deviation: 0.005

Sample information

Sample name: PHOSPHORYLATED AP2-NECAP CO-COMPLEX
Proteins: PHOSPHORYLATED AP2-NECAP CO-COMPLEX, AP-2 complex subunit alpha-2, AP-2 complex subunit beta, AP-2 complex subunit mu, AP-2 complex subunit sigma, Adaptin ear-binding coat-associated protein 2

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: RELION
Number of particles: 71571

Fitting

Initial atomic models: 2VGL, 1TQZ
Fitting protocol: rigid body
Target criteria: MAXIMUM LIKELIHOOD
Overall B value: 63.0
Refinement space: REAL
Details: STARTING MODEL WAS GENERATED BY DOCKING PDB ENTRIES 2VGL AND 1TQZ INTO CRYO-EM DENSITY AND MANUALLY EDITING SEQUENCE AND STRUCTURAl CHANGES. MODEL REFINEMENT WAS PERFORMED USING ROSETTA AND PHENIX.REAL_SPACE_REFINE

Imaging

Session
Microscope model: FEI TALOS ARCTICA
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 1.0
Nominal CS (mm): 2.70
Nominal magnification: 36000.0
Defocus max (nm): 2,500.00
Defocus min (nm): 600.00
Holder model: OTHER
Acquisition
Number of images: 944

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 1.00
Specimen support: GLOW DISCHARGE
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100
Details: 4 UL OF SAMPLE/GRID WAS BLOTTED FOR 4 SECONDS AND PLUNGE FROZEN IN LIQUID-NITROGEN COOLED ETHANE.