EMD-2232

Single-particle
12.4 Å
EMD-2232
3D View Gallery
Deposition: 01/11/2012
Map released: 03/04/2013
Last modified: 24/04/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-2232
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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 2ypw summary report (pdf.gz) Map and 2ypw FULL report (pdf.gz)
EMICSS annotations (xml)

Full-length structure of the bacterial pKM101 type IV secretion system core complex

EMD-2232

Single-particle
12.4 Å
EMD-2232
3D View Gallery
Deposition: 01/11/2012
Map released: 03/04/2013
Last modified: 24/04/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 5 mg/mL
Buffer
pH: 8.0
Details: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
Grid
Details: Lacey carbon grids
Vitrification
Cryogen name: ETHANE
Chamber humidity: 60%
Chamber temperature: 92 K
Instrument: OTHER
Method: blot 3 seconds 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: 2.1 mm
Nominal defocus: 1.25 µm - 3.5 µm
Nominal magnification: 66000.0
Calibrated magnification: 68100.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry liquid nitrogen-cooled cryo specimen holder
Details: 4000x4000 CCD
Temperature
Average: 95 K
Image Recording [1]
Detector category: CCD
Detector model: GENERIC GATAN
Sampling interval: 15 µm
Number of real images: 420
Average electron dose per image: 20 e/Å2
Bits per pixel: 8.0
Image processing [1]
Details: Particles picked with BOXER (EMAN)
Final reconstruction
Resolution: 12.4 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 3805
Algorithm: OTHER
Details: Final map were calculated from 3805 particles
⌯ Applied Symmetry
Point group: C14
Software [1]
Name Version Details
Imagic - -
Final 2D classification
Number of classes: 800
CTF correction
Details:Phase flipping, each CCD image
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of the pKM101 type IV secretion system core complex
Details: ::::EMDATABANK.org::::EMD-2232::::
⬡ Geometry
X Y Z
Dimensions 160 160 160
Origin -80 -79 -80
Spacing 160 160 160
Voxel size 2.22 Å 2.22 Å 2.22 Å
Contour list
Primary Level Source
True 0.45 AUTHOR