EMD-2170 Experiments and Validation

Thermococcus kodakaraensis 70S ribosome

Single particle reconstruction
Overview of EMD-2170
Sample name: Thermococcus kodakaraensis 70S ribosome
Organism: Thermococcus kodakarensis
Related EM entry by publication: EMD-2171, EMD-2172

Map parameters

Recommended contour level: 0.001 (emdb)
Number of grid points: 225 × 229 × 263
Voxel size: 3.31 × 3.31 × 3.31 Å
Minimum density: 0.00
Maximum density: 0.003
Average density: 0.00
Standard deviation: 0.00

Sample information

Sample name: Thermococcus kodakaraensis 70S ribosome
Ribosome: 70S ribosome

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: SPIDER
Number of particles: 10431
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
Nominal magnification: 90000.0
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 99
Scanner model: OTHER
Details: Eagle 4k CCD

Specimen

Preparation
Specimen state: particle
Staining procedure: 20 mM Hepes pH 7.5, 10 mM Mg(OAc)2, 30 mM NH4OAc, 4 mM beta-Mercaptoethanol
Vitrification
Apparatus: FEI VITROBOT MARK I
Cryogen: ETHANE
Humidity: 100
Protocol: Blot for 10 seconds before plunging, use 2 layers of filter paper
Details: Vitrification instrument: Vitrobot