EMD-2233
Subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase
EMD-2233
Single-particle8.5 Å
Deposition: 01/11/2012
Map released: 03/04/2013
Last modified: 24/04/2013
Concentration: 0.01
mg/mL
Buffer
pH: 8.0
Details: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
Details: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
Grid
Details: Continuous carbon-coated grids
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 92 K
Instrument: FEI VITROBOT MARK III
Method: blot 4 seconds before plunging
Chamber humidity: 100%
Chamber temperature: 92 K
Instrument: FEI VITROBOT MARK III
Method: blot 4 seconds before plunging
Microscope: FEI TECNAI 12
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.1 mm
Nominal defocus: 1.5 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
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.1 mm
Nominal defocus: 1.5 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: 262
Average electron dose per image: 20 e/Å2
Bits per pixel: 8.0
Detector model: GENERIC GATAN
Sampling interval: 15 µm
Number of real images: 262
Average electron dose per image: 20 e/Å2
Bits per pixel: 8.0
Details: Particles picked with BOXER (EMAN)
Final
reconstruction
Resolution: 8.5
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 5430
Algorithm: OTHER
Details: Final map was calculated from 5430 particles
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 5430
Algorithm: OTHER
Details: Final map was calculated from 5430 particles
⌯ Applied Symmetry
Point group:
C14
Software
[1]
Name | Version | Details |
---|---|---|
Imagic | - | - |
Final 2D classification
Number of classes:
1810
CTF correction
Details:Phase flipping, each CCD image
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Subnanometer reconstruction of the pKM101 type IV secretion system core complex digested with elastase
Details: ::::EMDATABANK.org::::EMD-2233::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Subnanometer reconstruction of the pKM101 type IV secretion system core complex digested with elastase
Details: ::::EMDATABANK.org::::EMD-2233::::
⬡ Geometry
X | Y | Z | |
---|---|---|---|
Dimensions | 160 | 160 | 160 |
Origin | -80 | -79 | -80 |
Spacing | 160 | 160 | 160 |
Voxel size | 2.08 Å | 2.08 Å | 2.08 Å |
Contour list
Primary | Level | Source |
---|---|---|
True | 0.23 | AUTHOR |