EMD-2172 Experiments and Validation

Methanococcus igneus 70S ribosome

Single particle reconstruction
Overview of EMD-2172
Sample name: Methanococcus igneus 70S ribosome
Organism: Methanotorris igneus
Related EM entry by publication: EMD-2170, EMD-2171

Map parameters

Recommended contour level: 2.17 (emdb)
Number of grid points: 368 × 368 × 368
Voxel size: 3.31 × 3.31 × 3.31 Å
Minimum density: -2.314
Maximum density: 6.458
Average density: 0.058
Standard deviation: 0.688

Sample information

Sample name: Methanococcus igneus 70S ribosome
Ribosome: Methanococcus igneus 70S ribosome

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: SPIDER
Number of particles: 8932
Reconstruction protocol: Single Particle
CTF correction: Wiener filter on 3D volumes

Fitting

Initial atomic model: 3CC2
Fitting software: UCSF Chimera
Fitting protocol: rigid body
Refinement space: REAL
Details: Protocol: Rigid-body fit into the density using UCSF Chimera built-in "Fit in Map". Rigid-body fit into the density using UCSF Chimera built-in "Fit in Map"

Imaging

Session
Microscope model: FEI TECNAI 12
Electron source: LAB6
Electron dose (e/A**2): 20.0
Nominal CS (mm): 2.00
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 99
Scanner model: OTHER
Details: Data collected on CCD

Specimen

Preparation
Specimen state: particle
Staining procedure: Blot for 10 seconds before plunging, use 2 layers of filter paper
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE
Humidity: 100
Protocol: Blot for 10 seconds before plunging, use 2 layers of filter paper
Details: Vitrification instrument: Vitrobot