9VBM | pdb_00009vbm

Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (dimer form)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Dimeric structure of DlGP
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3 microliters droplet, 0 seconds delay before blotting, 1.5 seconds blot, 0 second delay before plunging.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles110303
Reported Resolution (Å)3.19
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
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 (6k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL CRYO ARM 200
Minimum Defocus (nm)700
Maximum Defocus (nm)2200
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)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.7.0
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC4.7.0
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTcryoSPARC4.7.0
FINAL EULER ASSIGNMENTcryoSPARC4.7.0
RECONSTRUCTIONcryoSPARC4.7.0
MODEL REFINEMENTPHENIX1.21.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE1476535