EMD-5188

Single-particle
13.0 Å
EMD-5188
3D View Gallery
Deposition: 16/04/2010
Map released: 13/10/2010
Last modified: 06/03/2013
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5188
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 3iyq summary report (pdf.gz) Map and 3iyq FULL report (pdf.gz)
EMICSS annotations (xml)

tmRNA-SmpB: a journey to the center of the bacterial ribosome

EMD-5188

Single-particle
13.0 Å
EMD-5188
3D View Gallery
Deposition: 16/04/2010
Map released: 13/10/2010
Last modified: 06/03/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.5
Details: 5mM Hepes-KOH (pH 7.5), 10mM NH4Cl, 10mM MgOAc, 50mM KCl, 0.1mM EDTA and 6mM BetaME
Grid
Details: Quantifoil holey-carbon grids previously glow-discharged
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 100 K
Instrument: OTHER
Method: Blot for 5 seconds before plunging
Details: Vitrification instrument: vitrobot
Microscopy [1]
Microscope: JEOL 2200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 0.9 µm - 2.2 µm
Nominal magnification: 50000.0
Calibrated magnification: 45700.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Eucentric
Temperature
Average: 95 K
Specialist optics
Energy filter
Name: JEOL
Lower energy threshold: 0.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: NIKON SUPER COOLSCAN 9000
Sampling interval: 7.5 µm
Number of real images: 70
Bits per pixel: 8.0
Image processing [1]
Final reconstruction
Resolution: 13.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 49061
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
IMAGIC-V - -
CTF correction
Details:Each particle
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Structure of tmRNA-SMPB complex accomodated into a stalled bacterial ribosome
Details: ::::EMDATABANK.org::::EMD-5188::::
⬡ Geometry
X Y Z
Dimensions 128 128 128
Origin -64 -64 -64
Spacing 128 128 128
Voxel size 3.28 Å 3.28 Å 3.28 Å
Contour list
Primary Level Source
True 0.01 AUTHOR