EMD-3997

Single-particle
7.6 Å
EMD-3997
3D View Gallery
Deposition: 15/11/2017
Map released: 10/01/2018
Last modified: 28/03/2018
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-3997
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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)
EMICSS annotations (xml)

N2 and N3 ring of PilQ from Thermus thermophilus

EMD-3997

Single-particle
7.6 Å
EMD-3997
3D View Gallery
Deposition: 15/11/2017
Map released: 10/01/2018
Last modified: 28/03/2018
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 8.5
Grid
Mesh: 400
Model: Quantifoil R1.2/1.3
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON CONTINUOUS -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 70%
Chamber temperature: 283 K
Instrument: FEI VITROBOT MARK IV
Details: Blotting for 8-10 seconds.
Microscopy [1]
Microscope: JEOL 3200FSC
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 4.2 mm
Nominal magnification: 20000.0
Calibrated magnification: 30675.0
Specimen holder model: JEOL
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Specialist optics
Energy filter
Name: In-column Omega Filter
Lower energy threshold: 18 eV
Upper energy threshold: 18 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Frames per image: 2-45
Average exposure time: 9.0 s
Average electron dose per image: 33.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 7.6 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 2646
⌯ Applied Symmetry
Point group: C13
Software [1]
Name Version Details
FREALIGN - -
Startup model [1]
Type: INSILICO MODEL
Insilico model: A featureless cylinder generated in Xmipp 3.1
⦨ Initial angle assignment
Type: OTHER
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Details: The images of the subdomain containing the N2 and N3 rings after residual signal subtraction were recentered and placed in a smaller with our new program REP, followed by refinement by FREALIGN.
Software [1]
Name Version Details
FREALIGN - -
Particle selection [1]
Selected Ref. model Method Software Details
11457 - - - -
CTF correction
Software [1]
Name Version Details
CTFFIND 4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: None
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 324 324 324
Dimensions (Å) 528.12 528.12 528.12
Voxel size (Å) 1.63 1.63 1.63
Contour list
Primary Level Source
True 0.0385 AUTHOR