9QJ4 | pdb_00009qj4

Structure of the Complement classical and lectin pathway proconvertase, C4b2

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JTW
experimental model	PDB	3ERB
experimental model	PDB	2ODP

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.548
f_angle_d	0.827
f_chiral_restr	0.047
f_plane_restr	0.005
f_bond_d	0.004

Sample
Classical and lectin pathway C3 proconvertase

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	31895
Reported Resolution (Å)	3.9
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, 3ERB, 2I6Q)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

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

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v3.2/3
IMAGE ACQUISITION	EPU	2.10.0
CTF CORRECTION	cryoSPARC	v3.2/3
MODEL FITTING	UCSF ChimeraX	1.7
INITIAL EULER ASSIGNMENT	cryoSPARC	v3.2/3
FINAL EULER ASSIGNMENT	cryoSPARC	v3.2/3
CLASSIFICATION	cryoSPARC	v3.2/3
RECONSTRUCTION	cryoSPARC	v3.2/3
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		2647189

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.