EMD-9961

Single-particle
4.0 Å
EMD-9961
3D View Gallery
Deposition: 03/07/2019
Map released: 01/07/2020
Last modified: 23/12/2020
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-9961
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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 6kf4 summary report (pdf.gz) Map and 6kf4 FULL report (pdf.gz)
EMICSS annotations (xml)

Thermococcus kodakarensis RNA polymerase in complex with transcription factor E

EMD-9961

Single-particle
4.0 Å
EMD-9961
3D View Gallery
Deposition: 03/07/2019
Map released: 01/07/2020
Last modified: 23/12/2020
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.3 mg/mL
Buffer
pH: 8.0
Grid
Mesh: 200
Model: Quantifoil R1.2/1.3
Material: COPPER
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 278 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 0.002 mm
Nominal defocus: 1.5 µm - 3.5 µm
Nominal magnification: 47000.0
Calibrated magnification: 100000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: ZEMLIN TABLEAU
Specialist optics
SPH aberration_corrector: Image Cs corrector
Image Recording [1]
Detector model: FEI FALCON II (4k x 4k)
Detector mode: INTEGRATING
Frames per image: 1-30
Number of real images: 2698
Average exposure time: 1.8 s
Average electron dose per image: 63.0 e/Å2
Image processing [1]
Details: Movie frame data was subjected to motion correction to generate summed micrographs using MotionCor2.
Final reconstruction
Resolution: 4.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 252508
Algorithm: BACK PROJECTION
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: PDB ENTRY
PDB model: 4QIW
Details:PDB file was converted to EM map using e2pdb2mrc.py routine in EMAN2 software package. The reference map was lowpass filtered to 60 angstroms as a startup model.
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 2.1 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 2.1 -
Particle selection [1]
Selected Ref. model Method Software Details
1226339 - - - Approximately 20,000 particles were selected manually. 2D class averages from the manual-picked particles were used as a template for automated particle picking in Relion 2.1.
Final 3D classification
Number of classes: 8
Avg. number of members per classes: 51207.0
Software [1]
Name Version Details
RELION 2.1 -
CTF correction
Details: Defocus parameters were calculated from motion-corrected micrographs, using Gctf 1.06. Using the defocus parameters, Cs (0.003, after Cs image corrector tuning) and amplitude contrast (0.1), CTF phase flipping and amplitude correction was performed during the reconstruction using Relion 2.1.
Software [1]
Name Version Details
Gctf 1.06 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM single particle analysis 3D reconstruction of RNA polymerase (RNAP) from Thermococcus kodakarensis (Tko), in complex with transcription factor E (TFE)
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 176 176 176
Dimensions (Å) 246.4 246.4 246.4
Voxel size (Å) 1.4 1.4 1.4
Contour list
Primary Level Source
True 0.08 AUTHOR