8B0F | pdb_00008b0f

CryoEM structure of C5b8-CD59

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.6619
f_angle_d	0.7343
f_chiral_restr	0.0461
f_plane_restr	0.0096
f_bond_d	0.0034

Sample
C5b8-CD59
Sample Components
Complement components C5, C6, C7 and C8
CD59 glycoprotein

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	206782
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value	87
Fitting Procedure
Details	Initial rigid body fits were performed using UCSF Chimera and UCSF ChimeraX. Carbohydrates were added using Coot. Models were refined iteratively usin ...	Initial rigid body fits were performed using UCSF Chimera and UCSF ChimeraX. Carbohydrates were added using Coot. Models were refined iteratively using Isolde and Phenix Real Space Refine.

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2400
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
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.3.2
CTF CORRECTION	cryoSPARC	3.3.2
MODEL FITTING	UCSF ChimeraX
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.2
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.2
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.20.1-4887
MODEL REFINEMENT	ISOLDE	1.4
MODEL REFINEMENT	Coot	0.9.8.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1138825	CrYOLO neural network based particle picking, standard model, low threshold (0.01).