8XCS

Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH, AKG and NH4 in the initial stage of reaction


ELECTRON MICROSCOPY
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 277 K was flash-frozen 15-s after mixing GDH, NADP and glutamate solutions.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles160759
Reported Resolution (Å)2.63
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 Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTRELION4.0
FINAL EULER ASSIGNMENTRELION4.0
CLASSIFICATIONRELION4.0
RECONSTRUCTIONRELION4.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION5267415auto-picking with LoG-fiter inplemented in Relion