8XCY

Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the steady stage of reaction


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d3.689
f_angle_d0.483
f_chiral_restr0.043
f_plane_restr0.004
f_bond_d0.003
Sample
Hexamer of glutamate dehydrogenase in the presence of NADP and glutamate
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsThe sample solution kept at room temperature was flash-frozen 1-h after mixing GDH, NADP and glutamate solutions.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles86791
Reported Resolution (Å)2.91
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)1
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL CRYO ARM 300
Minimum Defocus (nm)400
Maximum Defocus (nm)47000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsGrid information as following: Company/model: Quantifoil Cu 1.2/1.3 Material:Cu Grid mesh: 200
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0beta
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTRELION4.0beta
FINAL EULER ASSIGNMENTRELION4.0beta
CLASSIFICATIONRELION4.0beta
RECONSTRUCTIONRELION4.0beta
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION6334528Auto-picking based on templates from manually picked GDH particles.