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R583A mutant of glycogen phosphorylase from Segatella copri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9L6I
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.343 f_angle_d 0.532 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Sample glycogen phosphorylase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 microliters droplet, 10 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 249469 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9L6I) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 200 Minimum Defocus (nm) 700 Maximum Defocus (nm) 2200 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) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.0 CTF CORRECTION cryoSPARC 4.6.0 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC 4.6.0 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.0 MODEL REFINEMENT PHENIX 1.19.2_4158
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE