EMD-9232

Helical reconstruction
2.7 Å
EMD-9232
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Deposition: 18/10/2018
Map released: 13/03/2019
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-9232
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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)
Map and PDB model 6mst summary report (pdf.gz) Map and 6mst FULL report (pdf.gz)
EMICSS annotations (xml)

Cryo-EM structure of human AA amyloid fibril

EMD-9232

Helical reconstruction
2.7 Å
EMD-9232
3D View Gallery
Deposition: 18/10/2018
Map released: 13/03/2019
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Helical reconstruction
Aggregation State: Helical Array
Specimen preparation [1]
Concentration: 0.2 mg/mL
Buffer
pH: 7.0
Buffer components [1]:
Name Formula Concentration ChEBI
- ddH2O -
Grid
Model: C-flat-1.2/1.3 4C
Material: COPPER
Details: 15 mA
Pretreatment
Type: GLOW DISCHARGE
Time: {'units': 's', 'valueOf_': '40'}
Atmosphere: OTHER
Pressure: 0.025 kPa
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 293 K
Instrument: FEI VITROBOT MARK III
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 50.0 µm
Nominal CS: 2.7 mm
Nominal defocus: -0.5 µm - -2.5 µm
Nominal magnification: 130000.0
Cooling holder cryogen: NITROGEN
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Average exposure time: 12.0 s
Average electron dose per image: 40.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 2.7 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 91872
⌯ Applied Symmetry
ΔΖ: 2.4 Å
ΔΦ: 0.79°
Axial symmetry: C1
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: NONE
⦩ Final angle assignment
Type: NOT APPLICABLE
Software [1]
Name Version Details
RELION 2.1 -
Segment selection [1]
Number selected Segment length Segment overlap Total filament length Details
93025 - - - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM reconstruction of human Serum Amyloid A fibrils, extracted from diseased human kidney. The fibril shows a helical rise of 2.40 A, a helical twist of 180.79 degree and a resolution of 2.7 A.
⬡ Geometry
X Y Z
Dimensions 270 270 270
Origin 0 0 0
Spacing 270 270 270
Voxel size 1.04 Å 1.04 Å 1.04 Å
Contour list
Primary Level Source
True 0.05 AUTHOR