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Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.326 f_angle_d 0.515 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Sample Dimer complex of glycine (de)carboxylating apo open form
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 1975829 Reported Resolution (Å) 2.32 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Cross-correlation coefficient Overall B Value 106.5 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model SHUIMU TOTEM 300S Minimum Defocus (nm) 1400 Maximum Defocus (nm) 1600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification 60000 Calibrated Magnification 60000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION CTFFIND 4.1 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3153680