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 8ZND | pdb_00008znd

Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH and a substrate in the steady stage of reaction


ELECTRON MICROSCOPY
Sample
Hexamer of W89F mutated glutamate dehydrogenase
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsThe sample solution was flash-frozen 2-h after mixing the protein solution and buffer solution.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles225530
Reported Resolution (Å)2.53
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL CRYO ARM 300
Minimum Defocus (nm)350
Maximum Defocus (nm)5000
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 CORRECTIONCTFFIND4.1.14
MODEL FITTINGPHENIX
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 CORRECTION3534400