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Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH and AKG in the steady stage of reaction
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.542 f_angle_d 0.438 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Sample Hexamer of glutamate dehydrogenase in the presence of NADP and glutamate
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details The sample solution kept at room temperature was flash-frozen 1-h after mixing GDH, NADP and glutamate solutions.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 136459 Reported Resolution (Å) 2.87 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 1
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 400 Maximum Defocus (nm) 47000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Grid information as following:
Company/model: Quantifoil Cu 1.2/1.3
Material:Cu
Grid mesh: 200
EM Software Task Software Package Version PARTICLE SELECTION RELION 4.0beta IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND MODEL FITTING Coot MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT RELION 4.0beta FINAL EULER ASSIGNMENT RELION 4.0beta CLASSIFICATION RELION 4.0beta RECONSTRUCTION RELION 4.0beta
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6334528 Auto-picking based on templates from manually picked GDH particles.