6Z7P | pdb_00006z7p

Composite model of the Caulobacter crescentus S-layer bound to the O-antigen of lipopolysaccharide

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N8P
experimental model	PDB	6T72

Sample
S-layer

Specimen Preparation
Sample Aggregation State	CELL
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	NITROGEN
Sample Vitrification Details	1.5 s blot

3D Reconstruction
Reconstruction Method	SUBTOMOGRAM AVERAGING
Number of Particles	51866
Reported Resolution (Å)	4.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Tomogram generation in IMOD using the NovaCTF implementation of Turonova and Briggs. Sub-tomogram averaging performed using the AV3 package (Friedrich ...	Tomogram generation in IMOD using the NovaCTF implementation of Turonova and Briggs. Sub-tomogram averaging performed using the AV3 package (Friedrich Foerster) applied to tubular specimens (Bharat et al, PLoS Biology, 2011)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5N8P, 6T72)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	USCF Chimera
Overall B Value
Fitting Procedure
Details	Initial rigid body fit of the C-terminal X-ray structure (PDB: 5N8P, amino acids 249-1046) and the N-terminal cryo-EM structure (PDB: 6T72, amino acid ...	Initial rigid body fit of the C-terminal X-ray structure (PDB: 5N8P, amino acids 249-1046) and the N-terminal cryo-EM structure (PDB: 6T72, amino acids 2-243) was performed in USCF Chimera. The missing amino acid linker was manually added suing Coot. The model was not refined against the map and all B-factors were set to zero due to resolution anisotropy.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	3.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	-2000
Maximum Defocus (nm)	-5000
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	105000
Calibrated Magnification	105000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
VOLUME SELECTION	RELION	1.4
IMAGE ACQUISITION	SerialEM
MODEL FITTING	UCSF Chimera	1.13
MODEL FITTING	Coot	0.9-pre

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Following Turonova and Briggs NovaCTF

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.