EMD-1080

Single-particle
11.5 Å
EMD-1080
3D View Gallery
Deposition: 06/05/2004
Map released: 12/05/2004
Last modified: 26/05/2011
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-1080
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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)

A 11.5 A single particle reconstruction of GroEL using EMAN.

EMD-1080

Single-particle
11.5 Å
EMD-1080
3D View Gallery
Deposition: 06/05/2004
Map released: 12/05/2004
Last modified: 26/05/2011
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 1.0 mg/mL
Vitrification
Cryogen name: ETHANE
Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Manual, gravity, plunger
Microscopy [1]
Microscope: JEOL 4000EX
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 400 kV
Nominal CS: 4.1 mm
Nominal defocus: 1.0 µm - 2.4 µm
Nominal magnification: 50000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: ZEISS SCAI
Sampling interval: 7 µm
Number of real images: 5
Average electron dose per image: 30 e/Å2
Bits per pixel: 8.0
Details: Data was median filtered to 14 microns/pixel after scanning.
Image processing [1]
Details: Note that class averages are EMAN-style reference-based, not MSA.
Final reconstruction
Resolution: 11.5 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 4916
Details:
⌯ Applied Symmetry
Point group: D7
Software [1]
Name Version Details
EMAN - -
Final 2D classification
Number of classes: 334
CTF correction
Details:Per particle phase flipping, amplitude correction during averaging
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: This is the volumetric data for our published 11.5 A resolution reconstruction of GroEL. Note that newer EMAN releases can refine the same data to ~9 A resolution.
Details: ::::EMDATABANK.org::::EMD-1080::::
⬡ Geometry
X Y Z
Dimensions 100 100 100
Origin -50 -50 -50
Spacing 100 100 100
Voxel size 2.7 Å 2.7 Å 2.7 Å
Contour list
Primary Level Source
True 0.852 -