EMD-6840

Single-particle
2.6 Å
EMD-6840
3D View Gallery
Deposition: 26/10/2017
Map released: 25/04/2018
Last modified: 25/04/2018
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-6840
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
EMICSS annotations (xml)

The first reconstruction of beta-galactosidase solved by cryoARM200

EMD-6840

Single-particle
2.6 Å
EMD-6840
3D View Gallery
Deposition: 26/10/2017
Map released: 25/04/2018
Last modified: 25/04/2018
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Details: This sample was monodisperse by adding 10 mM EDTA.
Buffer
pH: 8.0
Buffer components [4]:
Name Formula Concentration ChEBI
Tris C4H11NO3 25.0 mM
Sodium chloride NaCl 50.0 mM
Magnesium chloride MgCl2 2.0 mM
EDTA C10H16N2O8 10.0 mM
Grid
Mesh: 200
Model: Quantifoil R1.2/1.3
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: JEOL CRYO ARM 200
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
C2 aperture diameter: 100.0 µm
Nominal CS: 1.4 mm
Nominal defocus: 0.3 µm - 2.0 µm
Calibrated defocus: 0.248 µm - 2.167 µm
Nominal magnification: 60000.0
Calibrated magnification: 56497.0
Specimen holder model: JEOL
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Details: JEM-Z200FSC
Temperature
Minimum: 100.4 K
Maximum: 100.4 K
Image Recording [1]
Detector model: GATAN K2 IS (4k x 4k)
Dimensions: 3710 pixel x 3838 pixel
Sampling interval: 5.0 µm
Number of grids: 1
Number of real images: 2161
Average exposure time: 10.0 s
Average electron dose per image: 70.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 2.6 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 93975
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: D2
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-4116
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Number of reference projections: 9216
Angular sampling: 7.5 degrees
Software [1]
Name Version Details
RELION 2.1 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 2.1 -
Final 3D classification
Number of classes: 3
Software [1]
Name Version Details
RELION 2.1 -
CTF correction
Software [1]
Name Version Details
Gctf 1.06 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: First structure of the beta-galactosidase solved by cryoARM
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 240 240 240
Dimensions (Å) 212.4 212.4 212.4
Voxel size (Å) 0.885 0.885 0.885
Contour list
Primary Level Source
True 0.055 AUTHOR