EMD-5586 Experiments and Validation

An asymmetric unit map from Electron cryo-microscopy of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)

Single particle reconstruction
Overview of EMD-5586
Sample name: An asymmetry unit of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Organism: Haliotis diversicolor
Fitted atomic model: 3j32
Related EM entry by publication: EMD-1648, EMD-5585

Map parameters

Recommended contour level: 1.50 (author)
Number of grid points: 600 × 600 × 600
Voxel size: 1.02 × 1.02 × 1.02 Å
Minimum density: -0.071
Maximum density: 11.359
Average density: 0.006
Standard deviation: 0.111

Sample information

Sample name: An asymmetry unit of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Protein: hemocyanin isoform 1

Validation information

Experimental information

 

Image processing

Applied symmetry: D5
Software: EMAN1
Number of particles: 28641
Reconstruction protocol: projection matching
CTF correction: each micrograph

Imaging

Session
Microscope model: JEOL 3200FSC
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Energy filter: in column omega
Energy window (eV): 0.00
Nominal CS (mm): 4.10
Nominal magnification: 60000.0
Defocus max (nm): 3,600.00
Defocus min (nm): 500.00
Holder model: JEOL 3200FSC CRYOHOLDER
Details: MDS
Acquisition
Number of images: 784
Scanner model: NIKON SUPER COOLSCAN 9000
Sampling interval (μm): 6.3499999999999996

Specimen

Preparation
Specimen state: particle
Buffer: 0.2M NaCl, 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2
Specimen support: 400 mesh copper 1.2/1.3 quantifoil grid with continuous carbon support, glow discharged.
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE
Humidity: 100
Protocol: Blot for 2 seconds before plunging.