9Q0N | pdb_00009q0n

Cryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinosine-5'-monophosphate (6-meTIMP)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Ternary complex of PPAT and NUDT5 with 6-methylthioinosine-5'-monophosphate
Sample Components
PPAT tetramer
NUDT5 dimer
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles967122
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.3
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC4.3
MODEL FITTINGUCSF ChimeraX
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE
INITIAL EULER ASSIGNMENTcryoSPARC4.3
FINAL EULER ASSIGNMENTcryoSPARC4.3
CLASSIFICATIONcryoSPARC4.3
RECONSTRUCTIONcryoSPARC4.3
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY