EMD-5586
An asymmetric unit map from Electron cryo-microscopy of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
EMD-5586
Single-particle4.5 Å
Deposition: 19/02/2013
Map released: 17/04/2013
Last modified: 29/05/2013
Buffer
pH: 7.5
Details: 0.2M NaCl, 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2
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.
Chamber humidity: 100%
Instrument: FEI VITROBOT MARK III
Method: Blot for 2 seconds before plunging.
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
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
Average: 88 K
Maximum: 100 K
Specialist optics
Energy filter
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
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
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:
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
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::::
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 |