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Glutamate dehydrogenase in complex with NADH, closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MW9
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.81 f_angle_d 1.013 f_chiral_restr 0.275 f_bond_d 0.011 f_plane_restr 0.005
Sample Binary complex of bovine glutamate dehydrogenase with NADH Sample Components L-glutamate:NAD(P)+ oxidoreductase (deaminating)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot for 3-6 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 34926 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details (Single particle--Applied symmetry: D3) Refinement Type Symmetry Type POINT Point Symmetry D3
Map-Model Fitting and Refinement Id 1 (3MW9) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details REFINEMENT PROTOCOL--flexible
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment 2014-11-23 Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 Calibrated Magnification 73964 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION CTFFIND 3 MODEL FITTING Coot MODEL FITTING PHENIX MODEL FITTING Rosetta MODEL FITTING UCSF Chimera RECONSTRUCTION EMAN 2 RECONSTRUCTION RELION MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details Each micrograph