8PVU

Cryo-EM structure of DHS-ERK2 complex with 1:1 stoichiometry refined in C1 symmetry


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8A0E 
experimental modelPDB 4QTA 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d3.855
f_angle_d0.565
f_chiral_restr0.044
f_plane_restr0.005
f_bond_d0.004
Sample
Complex of DHS-ERK2 with 1:1 stoichiometry
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsblot time: 2 s, blot force: 0
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles146572
Reported Resolution (Å)3.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (8A0E, 8A0E, 8A0E, 8A0E, 4QTA)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)40.16
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)900
Maximum Defocus (nm)2400
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 SELECTIONcryoSPARC
IMAGE ACQUISITIONEPU2.10.0.1941REL
CTF CORRECTIONcryoSPARC
MODEL FITTINGUCSF ChimeraX
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION438Manually picked