9QDL | pdb_00009qdl

CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q00711 
in silico modelAlphaFoldAF-P21801 
in silico modelAlphaFoldAF-P33421 
in silico modelAlphaFoldAF-P37298 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.8811
f_angle_d0.5275
f_chiral_restr0.0407
f_plane_restr0.0047
f_bond_d0.0035
Sample
THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles149808
Reported Resolution (Å)3.15
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)18.8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)2700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE