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Complex of the hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI.
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
19221
Reported Resolution (Å)
7.6
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (3N75, 3NBX)
Refinement Space
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Local resolution estimation and subsequent filtering of maps were performed in Relion3.0. For fitting of atomic models in the resulting filtered maps, ...
Local resolution estimation and subsequent filtering of maps were performed in Relion3.0. For fitting of atomic models in the resulting filtered maps, we used the previously-determined X-ray structures of LdcI (PDB ID: 3N75) (Kanjee et al., 2011) and RavA (PDB ID: 3NBX) (El Bakkouri et al., 2010). In each map, two decameric LdcI molecules extracted from PDB 3N75 and one spiral RavA hexamer extracted from a continuous RavA helix generated from PDB 3NBX were fitted separately using iMODFIT (Lopez-Blanco and Chacon, 2013), followed by a single round of B-factor (ADP) refinement in Phenix.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
40
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
41270
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Data collection was performed on an FEI Polara microscope operated at 300 kV.
Movies of 40 frames were collected with a total exposure time of 8s and a total dose of 40e-/Angstrom^2 on a K2 summit direct electron detector (Gatan) at a magnification of 41270x, corresponding to 1.21 Angstrom/pixel at the specimen level.
EM Software
Task
Software Package
Version
PARTICLE SELECTION
EMAN2
IMAGE ACQUISITION
Latitude
CTF CORRECTION
Gctf
MODEL FITTING
iMODFIT
INITIAL EULER ASSIGNMENT
RELION
2.0
FINAL EULER ASSIGNMENT
RELION
2.0
CLASSIFICATION
RELION
2.0
RECONSTRUCTION
RELION
2.0
MODEL REFINEMENT
PHENIX
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
18902
The cleanded dataset contains 11866 particles. Dataset expansion (C5) resulted in a dataset containing 59330 particles.