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 6ZD0 | pdb_00006zd0

Disulfide-locked early prepore intermedilysin-CD59


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BIK 
Sample
Early prepore of intermedilysin-CD59
Sample Components
Thiol-activated cytolysin
CD59 glycoprotein
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification DetailsWait time of 60 s, blot time 2.5 s, blot force 3
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles51041
Reported Resolution (Å)4.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (4BIK)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsModel of ILY-CD59 was fit and refined into the central subunit density. A combination of rigid body fitting and global minimization with secondary str ...Model of ILY-CD59 was fit and refined into the central subunit density. A combination of rigid body fitting and global minimization with secondary structure restraints was used to fit and refine the central subunit model. Then the central subunit model was rigid body fit as one body into the neighbouring subunits to generate a 3 subunit oligomer model.
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)66
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1900
Maximum Defocus (nm)3100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPixel size 1.4 A
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4
MODEL FITTINGPHENIX
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION
FINAL EULER ASSIGNMENTRELION
CLASSIFICATIONRELION
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE