EMD-21983

Single-particle
3.3 Å
EMD-21983
3D View Gallery
Deposition: 17/05/2020
Map released: 10/06/2020
Last modified: 06/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-21983
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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 6x0o summary report (pdf.gz) Map and 6x0o FULL report (pdf.gz)
EMICSS annotations (xml)

Single-Particle Cryo-EM Structure of Arabinosyltransferase EmbB from Mycobacterium smegmatis

EMD-21983

Single-particle
3.3 Å
EMD-21983
3D View Gallery
Deposition: 17/05/2020
Map released: 10/06/2020
Last modified: 06/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 8 mg/mL
Buffer
pH: 7.5
Grid
Mesh: 300
Model: UltrAuFoil
Material: GOLD
Pretreatment
Type: PLASMA CLEANING
Time: 7 s
Atmosphere: OTHER
Support Film [1]
Material Topology Thickness
GOLD HOLEY ARRAY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 80%
Chamber temperature: 278 K
Instrument: LEICA EM GP
Microscopy [1]
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
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: ZEMLIN TABLEAU
Image Recording [2]
Detector model: FEI FALCON III (4k x 4k)
Detector mode: COUNTING
Number of grids: 1
Number of real images: 2158
Average exposure time: 86.4 s
Average electron dose per image: 78.02 e/Å2
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Number of grids: 1
Number of real images: 7833
Average exposure time: 8.0 s
Average electron dose per image: 77.53 e/Å2
Image processing [2]
Final reconstruction
Resolution: 3.3 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 57970
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
CryoSPARC 2 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: Ab initio model
Details:Ab initio model was generated in CryoSPARC
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Details: Non-uniform refinement in CryoSPARC was used.
Software [1]
Name Version Details
CryoSPARC 2 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Details: Non-uniform refinement in CryoSPARC was used.
Software [1]
Name Version Details
CryoSPARC 2 -
Particle selection [1]
Selected Ref. model Method Software Details
162271 - - - -
Final reconstruction
Resolution: 3.3 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 57970
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
CryoSPARC 2 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: Ab initio model
Details:Ab initio model was generated in CryoSPARC
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Details: Non-uniform refinement in CryoSPARC was used.
Software [1]
Name Version Details
CryoSPARC 2 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Details: Non-uniform refinement in CryoSPARC was used.
Software [1]
Name Version Details
CryoSPARC 2 -
Particle selection [1]
Selected Ref. model Method Software Details
700201 - - - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Density modified map
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 256 256 256
Dimensions (Å) 256.0 256.0 256.0
Voxel size (Å) 1.0 1.0 1.0
Contour list
Primary Level Source
True 0.325 AUTHOR