EMD-0152
RELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer using particles from micrographs tilted at 40 degrees in EMPIAR-10097
EMD-0152
Single-particle3.1 Å
Deposition: 31/07/2018Map released: 08/08/2018
Last modified: 28/04/2021
Concentration: 0.75
mg/mL
Buffer
pH: 7.4
Details: PBS Buffer
Details: PBS Buffer
Vitrification
Cryogen name: ETHANE
Chamber humidity: 80%
Instrument: GATAN CRYOPLUNGE 3
Details: 3 microliters of 0.75 mg/mL sample was added to a plasma-cleaned (Gatan Solarus) 1.2-micron-hole, 1.3-micron-spacing holey gold grid (made in-house) and plunge-frozen in liquid ethane using the Cryoplunge 3 system (Gatan) operating at 80% humidity, 298K ambient temperature..
Chamber humidity: 80%
Instrument: GATAN CRYOPLUNGE 3
Details: 3 microliters of 0.75 mg/mL sample was added to a plasma-cleaned (Gatan Solarus) 1.2-micron-hole, 1.3-micron-spacing holey gold grid (made in-house) and plunge-frozen in liquid ethane using the Cryoplunge 3 system (Gatan) operating at 80% humidity, 298K ambient temperature..
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: 1.0 µm - 3.5 µm
Nominal magnification: 22500.0
Calibrated magnification: 38167.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Details: In order to account for highly preferred orientations of the specimen, data were acquired using tilts of 40 degrees.
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.0 µm - 3.5 µm
Nominal magnification: 22500.0
Calibrated magnification: 38167.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Details: In order to account for highly preferred orientations of the specimen, data were acquired using tilts of 40 degrees.
Image Recording
[1]
Detector model:
GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3710 pixel x 3838 pixel
Frames per image: 1-100
Average electron dose per image: 82.0 e/Å2
Detector mode: COUNTING
Dimensions: 3710 pixel x 3838 pixel
Frames per image: 1-100
Average electron dose per image: 82.0 e/Å2
Final
reconstruction
Resolution: 3.1
Å
(
BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 151596
Algorithm: FOURIER SPACE
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 151596
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group:
C3
Software
[1]
| Name | Version | Details |
|---|---|---|
| RELION | 3.0 | - |
⦨ Initial angle
assignment
⦩ Final angle assignment
Particle selection
[1]
| Selected | Ref. model | Method | Software | Details |
|---|---|---|---|---|
| 608919 | - | - | - | - |
Final 3D classification
Software
[1]
| Name | Version | Details |
|---|---|---|
| RELION | 3.0 | - |
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Postprocessed map
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Postprocessed map
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Origin | 0 | 0 | 0 |
| Dimensions (px) | 216 | 216 | 216 |
| Dimensions (Å) | 282.96 | 282.96 | 282.96 |
| Voxel size (Å) | 1.31 | 1.31 | 1.31 |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 0.078 | AUTHOR |