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Cryo-EM structure of PCAT1 in the inward-facing narrow conformation under ATP turnover condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RY2
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.058 f_angle_d 0.559 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Sample Ternary complex of PCAT1 with its cleaved peptide substrate and ATP-Mg
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 80156 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4RY2) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 80 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 1.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.0 MODEL FITTING REFMAC ccp4i version 7.0 MODEL REFINEMENT Coot 0.8.9.2 INITIAL EULER ASSIGNMENT RELION 3.0 FINAL EULER ASSIGNMENT cryoSPARC 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION cryoSPARC 3.0 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 2800000