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Title:Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM
Authors:Guo Q, Goto S, Chen Y, Muto A, Himeno H, Deng H, Lei J, Gao N
Sample:Name immature ribosomal small subunit from rimM gene deleted E.coli strain treated with RimM in vitro
Method:Single particle reconstruction (15.3 angstroms resolution)
Red flagLatest update:2013-03-06
Sample
Sample name: Name immature ribosomal small subunit from rimM gene deleted E.coli strain treated with RimM in vitro
Experimental molecular weight of the sample: 0.8
Components:
ID Type Name Exp. MW (MDa) Theo. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1ribosome-prokaryotesmall subunit from rimm gene deleted E.coli strain0.80.8falseEscherichia coli
2proteinRimMtrueEscherichia coli
Experiment
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
7.5 mg/mL150 mM NH4Cl,10mM Tris-HCL,10mM MgCl2
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE100% KFEI VITROBOT MARK IVBlot for 1 seconds before plunging ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD mm1500 nm3800 nm59000FIELD EMISSION GUNFEI EAGLE (4k x 4k) mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
GATAN LIQUID NITROGEN°° eV K K K mrad20 e/Å201-JAN-2012
Processing
Protocol:Reference Projections
Software:Spider
CTF correction:Weiner filter
Number of particles:29012
Imposed symmetry:C1
Resolution by author:15.3 Å
Resolution method:FSC 0.5
Processing details:This is a classification volume (No. 2) using ML3D methods.
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
3OFA flexibleCross-correlationMDFFREALProtocol: Initial local fitting was done using Chimera and then MDFF was used for flexible fitting. ref: Trabuco, L.G., Villa, E., Mitra, K., Frank, J. and Schulten, K. (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure, 16, 673-683