EMD-5500 Experiments and Validation

Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM

Single particle reconstruction
Overview of EMD-5500
Sample name: immature ribosomal small subunit from rimm gene deleted E.coli strain
Organism: Escherichia coli
Fitted atomic model: 3j28

Map parameters

Recommended contour level: -2.80 (author)
Number of grid points: 125 × 125 × 125
Voxel size: 2.76 × 2.76 × 2.76 Å
Minimum density: -6.676
Maximum density: 4.191
Average density: -4.024
Standard deviation: 0.567

Sample information

Sample name: immature ribosomal small subunit from rimm gene deleted E.coli strain
Ribosome: small subunit from rimm gene deleted E.coli strain

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: Spider
Number of particles: 32152
Reconstruction protocol: Reference Projections
CTF correction: Weiner filter

Fitting

Initial atomic model: 3OFA
Used chain: A
Fitting software: MDFF
Fitting protocol: flexible
Refinement space: REAL
Details: Protocol: MDFF

Imaging

Session
Microscope model: FEI TECNAI F20
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Nominal magnification: 80000.0
Defocus max (nm): 4,000.00
Defocus min (nm): 1,300.00
Holder model: GATAN LIQUID NITROGEN

Specimen

Preparation
Specimen state: particle
Buffer: 150 mM NH4Cl,10mM Tris-HCL,10mM MgCl2
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100
Protocol: Blot for 2 seconds before plunging