7PEO

Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	42.751
r_dihedral_angle_2_deg	37.367
r_mcangle_it	29.166
r_dihedral_angle_4_deg	24.997
r_scbond_it	22.677
r_mcbond_it	17.993
r_dihedral_angle_3_deg	16.497
r_dihedral_angle_1_deg	6.471
r_angle_refined_deg	1.228
r_chiral_restr	0.102
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Sample
Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Vitrobot options: Blot time 4 seconds, Blot force -13,1, Wait time 10 seconds, Drain time 0.5 seconds,

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	158430
Reported Resolution (Å)	4.37
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The final map was obtained from 158,430 particles and post-processed using a soft mask focused on the inner fourteen subunits yielding a resolution of 4.37 A according to the gold standard Fourier shell correlation criterion of 0.143 (Scheres, 2012) with some anisotropy in Z as judged by directional FSCs (Tan et al., 2017)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6T72)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The atomic coordinates (PDB ID 6T72) of our previous cryo-EM structure (von Kugelgen et al., 2020) of the RsaANTD oligomer bound to the O-antigen of lipopolysaccharide (LPS) were rigid body fitted into the final post-processed map from Relion 3.0 (Zivanov et al., 2018) using UCSF Chimera (Pettersen et al., 2004). The resulting fitted model was subjected to real-space refinement using Refmac5 (Murshudov et al., 2011) inside the CCP-EM suite (Burnely et al., 2017), as described previously (von Kugelgen et al., 2020), using reference restraints of the initial structure (PDB ID 6T72) generated with PROSMART (Nicholls et al. 2012).

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	44.8

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	UCSF Chimera	1.13
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.0
CLASSIFICATION	RELION	3.0
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	REFMAC	5.8.0258

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.	545533	Initial Particles were extracted in a 2x down-sampled 150 pixel x 150 pixel box and classified using reference-free 2D-classification inside RELION 3.0.