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CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9YBZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.526 f_angle_d 0.7142 f_chiral_restr 0.0459 f_plane_restr 0.0063 f_bond_d 0.0036
Sample A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
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 71315 Reported Resolution (Å) 2.92 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (9YBZ, 9YBZ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value 81.41 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON I (4k x 4k) Electron Dose (electrons/Å**2) 80
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 2300 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 165000 Calibrated Magnification 98700 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.7.1 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC v4.7.1 MODEL FITTING UCSF ChimeraX 1.11.1 INITIAL EULER ASSIGNMENT cryoSPARC v4.7.1 FINAL EULER ASSIGNMENT cryoSPARC v4.7.1 CLASSIFICATION cryoSPARC v4.7.1 RECONSTRUCTION cryoSPARC v4.7.1 MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5739678 Particles selected after 2 rounds of 2D template selections