EMD-2171 Experiments and Validation

Staphylothermus marinus 50S ribosomal subunit

Single particle reconstruction
Overview of EMD-2171
Sample name: Staphylothermus marinus 50S ribosomal subunit
Organism: Staphylothermus marinus
Related EM entry by publication: EMD-2172, EMD-2170

Map parameters

Minimum density: -2.46
Maximum density: 5.88
Average density: 0.02
Standard deviation: 0.65
Recommended contour level: 3.61 (emdb)

Sample information

Sample name: Staphylothermus marinus 50S ribosomal subunit
Ribosome: Staphylothermus marinus 50S ribosomal subunit

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: SPIDER
Number of particles: 11142
Reconstruction protocol: Single Particle
CTF correction: Wiener filter on 3D volumes

Fitting

Initial atomic model: 3CC2
Fitting software: Chimera
Fitting protocol: rigid body
Refinement space: REAL
Details: Protocol: Rigid body. 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
Nominal magnification: 90000.0
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: 20 mM Hepes pH 7.5, 10 mM Mg(OAc)2, 30 mM NH4OAc, 4 mM beta-Mercaptoethanol
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