EMD-8728

Helical reconstruction
4.1 Å
EMD-8728
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Deposition: 10/05/2017
Map released: 14/03/2018
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8728
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 5vrf summary report (pdf.gz) Map and 5vrf FULL report (pdf.gz)
EMICSS annotations (xml)

CryoEM Structure of the Zinc Transporter YiiP from helical crystals

EMD-8728

Helical reconstruction
4.1 Å
EMD-8728
3D View Gallery
Deposition: 10/05/2017
Map released: 14/03/2018
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Helical reconstruction
Aggregation State: Helical Array
Specimen preparation [1]
Concentration: 0.6 mg/mL
Details: The protein was purified in 0.2% n-dodecyl beta-D-maltoside
Buffer
pH: 7.0
Buffer components [3]:
Name Formula Concentration ChEBI
Sodium chloride NaCl 100.0 mM
Magnesium chloride MgCl2 5.0 mM
Sodium azide NaN3 5.0 mM
Details: Buffer was changed twice per day.
Grid
Mesh: 400
Model: EMS
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Time: {'units': 's', 'valueOf_': '30'}
Atmosphere: OTHER
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Instrument: HOMEMADE PLUNGER
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.2 µm - 2.5 µm
Calibrated defocus: 1.0 µm - 5.4 µm
Nominal magnification: 22500.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3710 pixel x 3838 pixel
Frames per image: 2-16
Number of grids: 3
Number of real images: 2743
Average exposure time: 10.0 s
Average electron dose per image: 70.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 4.1 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 72333
⌯ Applied Symmetry
ΔΖ: 28.2 Å
ΔΦ: -17.0°
Axial symmetry: D5
Software [1]
Name Version Details
RELION 2.0 -
Startup model [1]
Type: OTHER
Details:A map was obtained previously with images acquired on a JEOL2100 microscope. This map was used as a startup model (That map was obtained as follow: we started with a noisy cylinder. Then, a first reconstruction was obtained with Helicon (from SPARX) and refined with Frealix).
⦩ Final angle assignment
Type: NOT APPLICABLE
Software [1]
Name Version Details
RELION 2.0 -
Segment selection [1]
Number selected Segment length Segment overlap Total filament length Details
141904 - - - 2293 filaments selected with SPARX/EMAN2, then windowed into 141,904 segments (450x450 pixel overlapping segments)
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Primary map
⬡ Geometry
X Y Z
Dimensions 131 131 131
Origin 0 0 0
Spacing 131 131 131
Voxel size 1.07 Å 1.07 Å 1.07 Å
Contour list
Primary Level Source
True 0.018 AUTHOR