EMD-5476 Experiments and Validation

Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11 Angstrom resolution

Single particle reconstruction
Overview of EMD-5476
Sample name: vacuolar-type ATPases
Organism: Saccharomyces cerevisiae

Map parameters

Recommended contour level: 0.76 (author)
Number of grid points: 256 × 256 × 256
Voxel size: 1.40 × 1.40 × 1.40 Å
Minimum density: -0.212
Maximum density: 1.763
Average density: 0.057
Standard deviation: 0.224

Sample information

Sample name: vacuolar-type ATPases
Protein: vacuolar-type ATPases

Validation information

Experimental information


Image processing

Applied symmetry: C1
Software: Search_Fspace, Refine_Fspace, Build_Fspace
Number of particles: 34448
Reconstruction protocol: Projection matching
CTF correction: Each particle

Segmentation and Mask

Mask 1
Mask name: emd_5476_msk.map
Annotation: A subunit 1
Mask 2
Mask name: emd_5476_msk_1.map
Annotation: A subunit 2
Mask 3
Mask name: emd_5476_msk_2.map
Annotation: A subunit 3
Mask 4
Mask name: emd_5476_msk_3.map
Annotation: B subunit 1
Mask 5
Mask name: emd_5476_msk_4.map
Annotation: B subunit 2
Mask 6
Mask name: emd_5476_msk_5.map
Annotation: B subunit 3
Mask 7
Mask name: emd_5476_msk_6.map
Annotation: C subunit
Mask 8
Mask name: emd_5476_msk_7.map
Annotation: DF subcomplex
Mask 9
Mask name: emd_5476_msk_8.map
Annotation: E subunit 1
Mask 10
Mask name: emd_5476_msk_9.map
Annotation: E subunit 2
Mask 11
Mask name: emd_5476_msk_10.map
Annotation: E subunit 3
Mask 12
Mask name: emd_5476_msk_11.map
Annotation: G subunit 1
Mask 13
Mask name: emd_5476_msk_12.map
Annotation: G subunit 2
Mask 14
Mask name: emd_5476_msk_13.map
Annotation: G subunit 3
Mask 15
Mask name: emd_5476_msk_14.map
Annotation: H subunit
Mask 16
Mask name: emd_5476_msk_15.map
Annotation: a subunit
Mask 17
Mask name: emd_5476_msk_16.map
Annotation: c-ring
Mask 18
Mask name: emd_5476_msk_17.map
Annotation: d subunit
Mask 19
Mask name: emd_5476_msk_18.map
Annotation: detergent/lipid plug


Microscope model: FEI TECNAI F20
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 12.0
Nominal CS (mm): 2.00
Nominal magnification: 50000.0
Defocus max (nm): 5,000.00
Defocus min (nm): 3,000.00
Number of images: 1000
Scanner model: ZEISS SCAI
Sampling interval (μm): 7.0


Specimen state: particle
Specimen concentration (mg/mL): 2.50
Buffer: 50 mM Tris-HCl, 150 mM NaCl, 0.03% w/v dodecylmaltoside
Specimen support: Quantifoil R2/2 glow discharged in air
Cryogen: ETHANE
Humidity: 100
Protocol: Blot for 20 seconds before freezing