EMD-2490
Structure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome
EMD-2490
Single-particle4.9 Å
Deposition: 20/10/2013
Map released: 25/12/2013
Last modified: 22/01/2014
Buffer
pH: 7.9
Details: 20 mM HEPES-KOH, 100 mM KCl, 1 mM DTT, 20 mM MgCl2
Details: 20 mM HEPES-KOH, 100 mM KCl, 1 mM DTT, 20 mM MgCl2
Grid
Details: 200 mesh Quantifoil R2/1 and R 2/2 holey carbon grids
Vitrification
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.5 µm - 3.3 µm
Nominal magnification: 75000.0
Calibrated magnification: 141510.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.5 µm - 3.3 µm
Nominal magnification: 75000.0
Calibrated magnification: 141510.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 3.6 µm
Nominal magnification: 59000.0
Calibrated magnification: 99290.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image Recording
[1]
Detector category:
CCD
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Detector model: FEI FALCON I (4k x 4k)
Sampling interval: 14 µm
Average electron dose per image: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Details: Particles were selected and extracted in batchboxer (EMAN 1.9).
Final
reconstruction
Resolution: 4.9
Å
(
BY AUTHOR)
Resolution method: OTHER
Number of images used: 232181
Algorithm: OTHER
Details: An initial reconstruction was obtained using the angular reconstitution approach in Imagic-5. For visualization purposes the final map was amplitude and MTF-corrected in RELION.
Resolution method: OTHER
Number of images used: 232181
Algorithm: OTHER
Details: An initial reconstruction was obtained using the angular reconstitution approach in Imagic-5. For visualization purposes the final map was amplitude and MTF-corrected in RELION.
⌯ Applied Symmetry
Point group:
C1
Software
[1]
Name | Version | Details |
---|---|---|
Spider, IMAGIC-5, CTFFIND3, RELION | - | - |
CTF correction
Details:Per detector frame
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Structure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome
Details: ::::EMDATABANK.org::::EMD-2490::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Structure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome
Details: ::::EMDATABANK.org::::EMD-2490::::
⬡ Geometry
X | Y | Z | |
---|---|---|---|
Dimensions | 256 | 256 | 256 |
Origin | 4 | 4 | 4 |
Spacing | 256 | 256 | 256 |
Voxel size | 1.41 Å | 1.41 Å | 1.41 Å |
Contour list
Primary | Level | Source |
---|---|---|
True | 11.0 | AUTHOR |