9OX9 | pdb_00009ox9

Cryo-EM structure of S. Mansoni p97 bound to CB-5083

ELECTRON MICROSCOPY

---

Sample
p97 Homohexamer bound to inhibitor CB-5083

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	174830
Reported Resolution (Å)	2.85
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Homogenous refinement with global CTF refinement and local motion correction. 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
Refinement Space
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details	Model built by ModelAngelo for one chain. Other chains were manually fitted in Chimera and merged.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	62

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2400
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	Topaz
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC
MODEL FITTING	Coot
MODEL FITTING	UCSF Chimera
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		968168	Topaz picking, trained using subset of micrographs