7T56

Cryo-EM structure of PCAT1 in the inward-facing intermediate conformation under ATP turnover condition


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RY2 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.565
f_angle_d0.545
f_chiral_restr0.041
f_bond_d0.003
f_plane_restr0.003
Sample
Ternary complex of PCAT1 with its cleaved peptide substrate and ATP-Mg
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles88549
Reported Resolution (Å)3.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (4RY2)
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value80
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)1.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
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 Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND4.0
MODEL FITTINGREFMACccp4i version 7.0
MODEL REFINEMENTCoot0.8.9.2
INITIAL EULER ASSIGNMENTRELION3.0
FINAL EULER ASSIGNMENTcryoSPARC3.0
CLASSIFICATIONRELION3.0
RECONSTRUCTIONcryoSPARC3.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY2800000