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 29YA | pdb_000029ya

Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer with one Rieske protein in the c position and one in the b position and quinone in the quinone oxidation site


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOther 
Sample
native dimeric cytochrome bc1 complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles20781
Reported Resolution (Å)2.69
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsInitial model placement (rigid-body) into a map was done in ChimeraX
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)40.22
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)900
Maximum Defocus (nm)2100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.7
IMAGE ACQUISITIONEPU2.10.0.1941REL
CTF CORRECTIONcryoSPARC4.7
MODEL FITTINGUCSF ChimeraX1.10
MODEL REFINEMENTCoot0.9.8
MODEL REFINEMENTPHENIX2.0
INITIAL EULER ASSIGNMENTcryoSPARC4.7
CLASSIFICATIONcryoSPARC4.7
RECONSTRUCTIONcryoSPARC4.7
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION25600002.56M (template) and 1.91M (TOPAZ)