ISDA: 6T72

ELECTRON MICROSCOPY

Sample

Structure of RsaA N-terminal domain bound to LPS

Specimen Preperation

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 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

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). 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/Å²)	43

Imaging Experiment

Date of Experiment	?
Temprature (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

Imaging Experiment

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.