EMD-8805

Subtomogram averaging
9.8 Å
EMD-8805
3D View Gallery
Deposition: 30/06/2017
Map released: 10/10/2018
Last modified: 29/01/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8805
Download
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)

80S ribsome from Oryctolagus cuniculus, class IV - with mid-rotated/swiveled 40S and eeF2, derived from EMPIAR-10064 using eClarity

EMD-8805

Subtomogram averaging
9.8 Å
EMD-8805
3D View Gallery
Deposition: 30/06/2017
Map released: 10/10/2018
Last modified: 29/01/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.6
Buffer components [3]:
Name Formula Concentration ChEBI
HEPES - 20.0 mM -
Potassium chloride KCl 50.0 mM
Magnesium chloride MgCl2 2.0 mM
Grid
Model: Quantifoil R2/1
Material: COPPER
Pretreatment
Type: PLASMA CLEANING
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 60%
Chamber temperature: 295 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: SPOT SCAN
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 2.4 µm - 3.6 µm
Details: Data collection 20 --> -60, 22 --> 60 degrees
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: INTEGRATING
Dimensions: 3838 pixel x 3710 pixel
Average electron dose per image: 1.5 e/Å2
Image processing [1]
Final reconstruction
Resolution: 9.8 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
EmClarity 1.0 Adapted single-particle wiener filter
⦩ Final angle assignment
Type: OTHER
Details: 3D refinement with two half-sets fully separated after template matching, at which point the FSC 0.5 was 3.6 nanometers. Reference and subtomograms filtered dynamically according to the FSC at each cycle using the FOM approach.
Software [1]
Name Version Details
EmClarity 1.0 -
Final 3D classification
Number of classes: 5
Avg. number of members per classes: 500.0
Details: 3,090 total subtomograms were assigned to 5 separate classes using multi-scale PCA with full-3dCTF compensated estimators. 1.0,1.6,2.4,5.4 nm were the length-scales used for the msPCA.
Software [1]
Name Version Details
EmClarity 1.0 -
Extraction
Number of images used: 3090
CTF correction
Details:Phases corrected on the projections by multiplying by the CTF in tiles compensating for the defocus gradient in tilted images.
Software [1]
Name Version Details
EmClarity 1.0 Included astigmatism and per-tilt CTF determination
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Rabbit 80S ribosome derived from EMPIAR-10064 using emClarity. Mid-rotated/swiveled 40S with eeF2.
⬡ Geometry
X Y Z
Dimensions 336 336 336
Origin 0 0 0
Spacing 336 336 336
Voxel size 2.62 Å 2.62 Å 2.62 Å
Contour list
Primary Level Source
True 2.0 AUTHOR