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Cryo-EM structure of the Human SHMT1-RNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJ4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.0366 f_angle_d 0.4104 f_chiral_restr 0.0353 f_plane_restr 0.003 f_bond_d 0.0015
Sample human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blotted for 4 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 94430 Reported Resolution (Å) 3.52 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (1BJ4) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 132 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification 120000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION EPU 2.8 CTF CORRECTION CTFFIND 4 MODEL FITTING UCSF Chimera MODEL FITTING Coot 0.9.6 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1-17-1-3660
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4900000