7P06

Cryo-EM structure of Pdr5 from Saccharomyces cerevisiae in outward-facing conformation with ADP-orthovanadate/ATP


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.733
f_angle_d0.609
f_chiral_restr0.065
f_bond_d0.005
f_plane_restr0.005
Sample
Cryo-EM structure of Pdr5 from Saccharomyces cerevisiae in outward-facing conformation with ADP-orthovanadate/ATP
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles55155
Reported Resolution (Å)3.77
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)48.13
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX1.18.2
INITIAL EULER ASSIGNMENTcryoSPARC3.0
FINAL EULER ASSIGNMENTcryoSPARC3.0
CLASSIFICATIONcryoSPARC3.0
RECONSTRUCTIONcryoSPARC3.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION