EMD-3531

Single-particle
3.2 Å
EMD-3531
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Deposition: 10/12/2016
Map released: 11/01/2017
Last modified: 15/05/2024
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EMD-3531
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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)

Cryo-EM reconstruction of the large subunit of the chloroplast ribosome

EMD-3531

Single-particle
3.2 Å
EMD-3531
3D View Gallery
Deposition: 10/12/2016
Map released: 11/01/2017
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.12 mg/mL
Buffer
pH: 7.6
Buffer components [6]:
Name Formula Concentration ChEBI
Tris hydrochloride Tris-HCl 25.0 mM
Potassium chloride KCl 25.0 mM
Magnesium acetate Mg(CH3COO)2 25.0 mM
Dithiothreitol DTT 2.0 mM
Spermine - 0.05 mM -
Spermidine - 2.0 mM -
Grid
Model: Quantifoil R2/2
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON CONTINUOUS -
Vitrification
Cryogen name: ETHANE-PROPANE
Chamber humidity: 100%
Chamber temperature: 278 K
Instrument: FEI VITROBOT MARK I
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 0.8 µm - 3.5 µm
Nominal magnification: 59000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording [1]
Detector model: FEI FALCON II (4k x 4k)
Detector mode: INTEGRATING
Frames per image: 2-8
Number of real images: 2796
Average electron dose per image: 20.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.2 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 154332
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 1.4 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-2847
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 1.4 -
Particle selection [1]
Selected Ref. model Method Software Details
326094 - - - -
Final 3D classification
Software [1]
Name Version Details
RELION 1.4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM reconstruction of the 50S large subunit of the chloroplast ribosome
⬡ Geometry
X Y Z
Dimensions 320 320 320
Origin 0 0 0
Spacing 320 320 320
Voxel size 1.39 Å 1.39 Å 1.39 Å
Contour list
Primary Level Source
True 0.08 AUTHOR