Experiment: 11MG

Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XWJ

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.171
f_angle_d	0.816
f_chiral_restr	0.049
f_plane_restr	0.006
f_bond_d	0.004

Sample
Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1

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	143730
Reported Resolution (Å)	2.88
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (2XWJ)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	Initial docking of starting model performed in ChimeraX. Flexible/Refinement performed with Phenix Real-Space Refinement. Coot used for manual fitting ...	Initial docking of starting model performed in ChimeraX. Flexible/Refinement performed with Phenix Real-Space Refinement. Coot used for manual fitting and inspection.

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	43.36

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	300
Maximum Defocus (nm)	2100
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
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.7.1
IMAGE ACQUISITION	EPU	3.14
CTF CORRECTION	cryoSPARC	4.7.1
MODEL FITTING	Coot	0.9.8.96
INITIAL EULER ASSIGNMENT	cryoSPARC	4.7.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.7.1
CLASSIFICATION	cryoSPARC	4.7.1
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF estimation	1475831	Automated particle picking (Blob and Template picker, CryoSPARC) with manual inspection and micrograph junk detector