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Cryo-EM Structure of Human Serine Hydroxymethyltransferase, isoform 2 (SHMT2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AQL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.5658 f_angle_d 1.9334 f_chiral_restr 0.0948 f_plane_restr 0.0311 f_bond_d 0.0112
Sample SHMT2 in the form of PLP internal aldimine
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 146577 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D2
Map-Model Fitting and Refinement Id 1 (8aql) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.0.3 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.0.3 MODEL FITTING Coot 0.9.8 MODEL REFINEMENT PHENIX 1.20 INITIAL EULER ASSIGNMENT cryoSPARC 4.0.3 FINAL EULER ASSIGNMENT cryoSPARC 4.0.3 CLASSIFICATION cryoSPARC 4.0.3 RECONSTRUCTION cryoSPARC 4.0.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE