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Structure of the RsaA N-terminal domain bound to LPS
ELECTRON MICROSCOPY
Sample
Structure of RsaA N-terminal domain bound to LPS
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Vitrobot options:
Blot time 3 seconds,
Blot force -13,1,
Wait time 10 seconds,
Drain time 0.5 seconds,
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
115776
Reported Resolution (Å)
3.7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Particles from two main 3D classes containing 21 or 20 RsaA subunits were combined for a focused 3D auto refinement on the central 14 subunits using t ...
Particles from two main 3D classes containing 21 or 20 RsaA subunits were combined for a focused 3D auto refinement on the central 14 subunits using the output from the 3D classification as a starting model. The final map was obtained from 115,776 particles and post-processed using a soft mask focused on the inner fourteen subunits.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
BACKBONE TRACE
Refinement Target
Best fit
Overall B Value
85.819
Fitting Procedure
Details
The carbon backbone of the RsaA protein was manually traced through a single subunit of the cryo-EM density using Coot (Emsley et al., 2010). Initiall ...
The carbon backbone of the RsaA protein was manually traced through a single subunit of the cryo-EM density using Coot (Emsley et al., 2010). Initially, side chains were assigned in regions with density corresponding to characteristic aromatic residues allowing us to deduce the register of the amino acid sequence in the map. Side chains for residues 2-243 of RsaA were thus assigned unambiguously and the structure was refined and manually rebuilt using Refmac5 (Murshudov et al., 2011) inside the CCP-EM (Burnley et al., 2017) software suite and Coot.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
43
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
-1000
Maximum Defocus (nm)
-4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
130000
Calibrated Magnification
130000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EPU software
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
3.0
IMAGE ACQUISITION
EPU
CTF CORRECTION
CTFFIND
4.1.13
MODEL FITTING
Coot
0.9-pre
INITIAL EULER ASSIGNMENT
RELION
3.0
FINAL EULER ASSIGNMENT
RELION
3.0
CLASSIFICATION
RELION
3.0
RECONSTRUCTION
RELION
3.0
MODEL REFINEMENT
REFMAC
5
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included.
129633
Particles were automatically picked from the motion and CTF corrected micrographs using the AutoPick function in Relion 3.0 (Zivanov et al., 2018).
As particle reference a 3 dimensional reconstruction from an earlier dataset with different pixelsize was used which was reconstructed using an unbiased subtomogram average structure of the same sample.