EMD-2275
Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles
EMD-2275
Single-particle4.5 Å
Deposition: 08/01/2013
Map released: 23/01/2013
Last modified: 03/07/2013
Concentration: 0.3
mg/mL
Buffer
pH: 7.45
Details: 3mM Hepes-KOH, 6.6 mM Tris-acetate pH 7.2, 3 mM NH4Cl, 6.6 mM NH4-acetate, 48 mM K-acetate, 4 mM Mg-acetate, 2.4 mM DTT
Details: 3mM Hepes-KOH, 6.6 mM Tris-acetate pH 7.2, 3 mM NH4Cl, 6.6 mM NH4-acetate, 48 mM K-acetate, 4 mM Mg-acetate, 2.4 mM DTT
Grid
Details: Quantifoil grids (2/2) with 3 nm thin carbon on top
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 90 K
Instrument: FEI VITROBOT MARK II
Method: Blot 2.5 seconds before plunging
Chamber humidity: 100%
Chamber temperature: 90 K
Instrument: FEI VITROBOT MARK II
Method: Blot 2.5 seconds before plunging
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2 mm
Nominal defocus: 1.191 µm - 3.44 µm
Nominal magnification: 59000.0
Calibrated magnification: 79096.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2 mm
Nominal defocus: 1.191 µm - 3.44 µm
Nominal magnification: 59000.0
Calibrated magnification: 79096.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification, Electron beam tilt params: )
Temperature
Minimum: 80
K
Average: 85 K
Maximum: 90 K
Average: 85 K
Maximum: 90 K
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Number of real images: 200
Average electron dose per image: 16 e/Å2
Details: Every image is the average of sixteen frames recorded by the direct electron detector
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Number of real images: 200
Average electron dose per image: 16 e/Å2
Details: Every image is the average of sixteen frames recorded by the direct electron detector
Details: Use a newly developed statistical movie processing to compensate for beam-induced movement
Final
reconstruction
Resolution: 4.5
Å
(
BY AUTHOR)
Resolution method: OTHER
Number of images used: 35813
Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement
Resolution method: OTHER
Number of images used: 35813
Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement
⌯ Applied Symmetry
Point group:
C1
Software
[1]
Name | Version | Details |
---|---|---|
CTFFIND3, RELION | - | - |
CTF correction
Details:Each image
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of S.cereviseae 80S ribosome (conformation 1)
Details: ::::EMDATABANK.org::::EMD-2275::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of S.cereviseae 80S ribosome (conformation 1)
Details: ::::EMDATABANK.org::::EMD-2275::::
⬡ Geometry
X | Y | Z | |
---|---|---|---|
Dimensions | 240 | 240 | 240 |
Origin | -120 | -120 | -120 |
Spacing | 240 | 240 | 240 |
Voxel size | 1.77 Å | 1.77 Å | 1.77 Å |
Contour list
Primary | Level | Source |
---|---|---|
True | 0.3 | AUTHOR |