Experiment: 9P00

Cryo-EM structure of apo S. Mansoni p97

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9OX9

Sample
Homohexamer of p97

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	478635
Reported Resolution (Å)	2.72
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Homogenous refinement with global CTF refinement. The map was also sharpened by deepEMhancer to obtain final map used for modeling.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C6

Map-Model Fitting and Refinement
Id	1 (9OX9)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	Single chain ModelAngelo model built in PDB 9OX9 was docked into this map, and undergone manual modeling in Coot. The rest of the chains were built us ...	Single chain ModelAngelo model built in PDB 9OX9 was docked into this map, and undergone manual modeling in Coot. The rest of the chains were built using molrep in CCP-EM and refined.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC
MODEL FITTING	UCSF ChimeraX
MODEL FITTING	Coot
MODEL FITTING	ISOLDE
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	MOLREP
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1949076	Template picking with CB-5083-bound map