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Glutamate dehydrogenase in complex with NADH and GTP, open 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 6.461 f_angle_d 1.086 f_chiral_restr 0.379 f_bond_d 0.01 f_plane_restr 0.004
Sample Ternary complex of bovine glutamate dehydrogenase with GTP and 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 14793 Reported Resolution (Å) 3.6 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 2014-07-27 Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 5000 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 78426 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