EMD-6337

Single-particle
3.8 Å
EMD-6337
3D View Gallery
Deposition: 07/05/2015
Map released: 20/05/2015
Last modified: 19/08/2015
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-6337
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 5a22 summary report (pdf.gz) Map and 5a22 FULL report (pdf.gz)
EMICSS annotations (xml)

Structure of the L-protein of vesicular stomatitis virus from electron cryomicroscopy

EMD-6337

Single-particle
3.8 Å
EMD-6337
3D View Gallery
Deposition: 07/05/2015
Map released: 20/05/2015
Last modified: 19/08/2015
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.35 mg/mL
Buffer
pH: 7.4
Details: 25 mM HEPES, 250 mM NaCl, 6 mM MgSO4, 0.5 mM TCEP
Grid
Details: 400 mesh Quantifoil R1.2/1.3 Cu grid
Vitrification
Cryogen name: ETHANE
Chamber humidity: 65%
Instrument: FEI VITROBOT MARK I
Method: Blot time 2 seconds, drain time 1 second before plunging
Microscopy [1]
Microscope: FEI TECNAI F20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 0.9 µm - 2.3 µm
Nominal magnification: 29000.0
Calibrated magnification: 40410.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: CT3500
Details: Beam intensity: 8 electrons/pixel/s Movie mode: 30 frames, 5 frames/s
Image Recording [1]
Detector category: CCD
Detector model: GATAN K2 (4k x 4k)
Sampling interval: 5 µm
Number of real images: 1272
Average electron dose per image: 31 e/Å2
Details: Images are the sums of all 30 aligned movie frames (high dose) or frames 3 - 12 (low-dose).
Image processing [1]
Details: An initial map was obtained with EMAN2, IMAGIC, and TIGRIS. CTF was determined using CTFFIND3. Refinement and classification were done using Frealign.
Final reconstruction
Resolution: 3.8 Å ( BY AUTHOR)
Resolution method: OTHER
Number of images used: 74940
Algorithm: OTHER
Details: The final map represents the best class out of three classes.
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
EMAN2, IMAGIC, Frealign - -
Final 2D classification
Number of classes: 3
CTF correction
Details: Each particle
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of the L-protein of vesicular stomatitis virus
Details: ::::EMDATABANK.org::::EMD-6337::::
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 120 120 120
Dimensions (Å) 148.44 148.44 148.44
Voxel size (Å) 1.237 1.237 1.237
Contour list
Primary Level Source
True 1.2 AUTHOR