EMD-5586

Single-particle
4.5 Å
EMD-5586 Deposition: 19/02/2013
Map released: 17/04/2013
Last modified: 29/05/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5586

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

EMD-5586

Single-particle
4.5 Å
EMD-5586 Deposition: 19/02/2013
Map released: 17/04/2013
Last modified: 29/05/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.5
Details: 0.2M NaCl, 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2
Grid
Details: 400 mesh copper 1.2/1.3 quantifoil grid with continuous carbon support, glow discharged.
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Instrument: FEI VITROBOT MARK III
Method: Blot for 2 seconds before plunging.
Microscopy [1]
Microscope: JEOL 3200FSC
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 4.1 mm
Nominal defocus: 0.5 µm - 3.6 µm
Nominal magnification: 60000.0
Specimen holder model: JEOL 3200FSC CRYOHOLDER
Specimen holder details: Liquid N2 cooled
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 400,000 nominal magnification, Electron beam tilt params: )
Details: MDS
Temperature
Minimum: 80 K
Average: 88 K
Maximum: 100 K
Specialist optics
Energy filter
Name: In column omega
Lower energy threshold: 0.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: NIKON SUPER COOLSCAN 9000
Sampling interval: 6.35 µm
Number of real images: 784
Average electron dose per image: 20 e/Å2
Bits per pixel: 16.0
Image processing [1]
Details: Processed with EMAN1 followed by segmentation of asymmetric unit.
Final reconstruction
Resolution: 4.5 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 28641
Algorithm: OTHER
Details:
Applied Symmetry
Point group: D5
Software [1]
Name Version Details
EMAN1 - -
CTF correction
Details:Each micrograph
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Asymmetric unit map segmented from the reconstruction of isolated Haliotis diversicolor molluscan hemocyanin isoform 1
Details: ::::EMDATABANK.org::::EMD-5586::::
Geometry
X Y Z
Dimensions 600 600 600
Origin -300 -300 -300
Spacing 600 600 600
Voxel size 1.02 Å 1.02 Å 1.02 Å
Contour list
Primary Level Source
True 1.5 AUTHOR