EMD-0408

Single-particle
3.2 Å
EMD-0408
3D View Gallery
Deposition: 06/12/2018
Map released: 13/02/2019
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-0408
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

Single-particle cryo-EM reconstruction of human methemoglobin using 200 keV, state 2

EMD-0408

Single-particle
3.2 Å
EMD-0408
3D View Gallery
Deposition: 06/12/2018
Map released: 13/02/2019
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 12 mg/mL
Details: Lyophilized human methemoglobin (Sigma Aldrich) was solubilized in PBS pH 7.4.
Buffer
pH: 7.4
Buffer components [3]:
Name Formula Concentration ChEBI
Phosphate - 10.0 mM -
Sodium chloride NaCl 137.0 mM
Potassium Chloride KCl 2.7 mM
Grid
Mesh: 300
Model: Quantifoil, UltrAuFoil, R1.2/1.3
Material: GOLD
Details: Grids were plasma cleaned using a Solarus plasma cleaner (Gatan, Inc.)
Pretreatment
Type: PLASMA CLEANING
Time: 6 s
Atmosphere: OTHER
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 277.15 K
Instrument: HOMEMADE PLUNGER
Details: Sample was manually blotted for 4-5 seconds using Whatman No. 1 filter paper immediately prior to plunge-freezing..
Microscopy [1]
Microscope: FEI TALOS ARCTICA
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 5.0 µm - 16.0 µm
Nominal magnification: 73000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3710 pixel x 3838 pixel
Frames per image: 1-44
Number of grids: 1
Number of real images: 1673
Average exposure time: 11.0 s
Average electron dose per image: 69.0 e/Å2
Image processing [1]
Details: Counting mode, 250 ms frames, exposure rate of ~1.95 e-/pix/sec, total exposure of ~69 e-/angstrom-2 (1.57 e-/angstrom-2/frame).
Final reconstruction
Resolution: 3.2 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 11501
Algorithm: BACK PROJECTION
Details:
⌯ Applied Symmetry
Point group: C2
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: OTHER
Details:An ab initio model was generated from 160,169 template-picked particles using cryoSPARC and low-pass filtered to 30 A for use as an initial model for 3D refinement.
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 2.1 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 2.1 -
Particle selection [1]
Selected Ref. model Method Software Details
1615738 - - - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Single-particle cryo-EM reconstruction of human methemoglobin, state 2 (sharpened)
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 256 256 256
Dimensions (Å) 142.976 142.976 142.976
Voxel size (Å) 0.5585 0.5585 0.5585
Contour list
Primary Level Source
True 0.045 AUTHOR