Experiment: 9VCA

Binding site between C-reactive protein and c2cc monoclonal antibody

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HC3
experimental model	PDB	7PKE

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.2669
f_angle_d	0.8194
f_chiral_restr	0.0535
f_plane_restr	0.0071
f_bond_d	0.0061

Sample
Asymmetric unit of D5-symmetric complex composed of two pentameric C-reactive proteins interlinked with five monoclonal IgG antibodies
Sample Components
Human C-reactive protein
Monoclonal antibody

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	1434575
Reported Resolution (Å)	2.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The resolution estimated within a soft mask covering one pCRP chain and one Fab fragment. The number of particles provided after the D5 symmetry expa ...	The resolution estimated within a soft mask covering one pCRP chain and one Fab fragment. The number of particles provided after the D5 symmetry expansion
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3HC3, 7PKE)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	54

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
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	4.6
CTF CORRECTION	cryoSPARC	4.6
MODEL FITTING	Coot	0.9
MODEL REFINEMENT	ISOLDE	1.8
MODEL REFINEMENT	PHENIX	1.20
INITIAL EULER ASSIGNMENT	cryoSPARC	4.6
FINAL EULER ASSIGNMENT	cryoSPARC	4.6
RECONSTRUCTION	cryoSPARC	4.6

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		286000