8S32 | pdb_00008s32

GroEL with bound GroTAC peptide


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOther 
Sample
A complex of GroEL with GroTAC peptide
Sample Components
GroEL
GroTAC
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles203031
Reported Resolution (Å)2.45
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD7
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target0.88
Overall B Value
Fitting Procedure
DetailsThe C-alpha model was obtained by two rounds of ab initio modeling using machine learning-based ModelAngelo 1.09 software. The incorrectly assigned Gr ...The C-alpha model was obtained by two rounds of ab initio modeling using machine learning-based ModelAngelo 1.09 software. The incorrectly assigned GroEL residues were then manually corrected. The C-alpha trace of the GroTAC peptide was initially constructed by ModelAngelo, with residue identities suggested through a comparison to the 1MNF PDB structure. The reconstruction to full-atom was performed using cg2all 1.5 software. The first stage of refinement was done in Coot (0.9.8.5). The final refinement stage involved two rounds of phenix.real_space_refine (Phenix 1.21.5207).
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification240000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.3
IMAGE ACQUISITIONEPU3.4
CTF CORRECTIONcryoSPARC4.3
INITIAL EULER ASSIGNMENTcryoSPARC4.4
FINAL EULER ASSIGNMENTcryoSPARC4.4
CLASSIFICATIONcryoSPARC4.4
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTCoot0.9.8.5
MODEL REFINEMENTPHENIX1.21.5207
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION350383