9QPY | pdb_00009qpy

Structure of the Complement classical and lectin pathway C3 convertase

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JTW
experimental model	PDB	7B2Q
experimental model	PDB	2ODP

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.274
f_angle_d	0.66
f_chiral_restr	0.045
f_plane_restr	0.004
f_bond_d	0.003

Sample
Classical and lectin pathway C3 convertase

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	17283
Reported Resolution (Å)	4.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5JTW, 5JTW, 5JTW, 7B2Q, 2I6Q)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS TALOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v4.2.0/4
IMAGE ACQUISITION	EPU	2.10.0
CTF CORRECTION	cryoSPARC	v4.2.0/4
MODEL FITTING	UCSF ChimeraX	1.7
INITIAL EULER ASSIGNMENT	cryoSPARC	v4.2.0/4
FINAL EULER ASSIGNMENT	cryoSPARC	v4.2.0/4
CLASSIFICATION	cryoSPARC	v4.2.0/4
RECONSTRUCTION	cryoSPARC	v4.2.0/4
MODEL REFINEMENT	PHENIX	2.21.1
MODEL REFINEMENT	Coot	0.9.8.94

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE

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.