4A8C

Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3STJ 
Sample
ESCHERICHIA COLI DEGQ 12- MER IN COMPLEX WITH A BINDING PEPTIDE
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles29432
Reported Resolution (Å)7.5
Resolution Method
Other DetailsDEGQ 12-MER WERE OBTAINED IN PRESENCE OF A PEPTIDE. THE PEPTIDE SEQUENCE IS SPMFKGVLDMMYGGMRGYQV THE NUMBER OF PEPTIDES BOUND TO DEGQ 12-MER IS UNKNOW ...DEGQ 12-MER WERE OBTAINED IN PRESENCE OF A PEPTIDE. THE PEPTIDE SEQUENCE IS SPMFKGVLDMMYGGMRGYQV THE NUMBER OF PEPTIDES BOUND TO DEGQ 12-MER IS UNKNOWN. THE PEPTIDES ARE NOT MODELLED DUE TO THE RESOLUTION OF THE MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1983. (DEPOSITION ID: 10374).
Refinement Type
Symmetry TypePOINT
Point SymmetryD3
Map-Model Fitting and Refinement
Id1 (3STJ)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsMETHOD--RIGID BODY AND FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)15
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)91
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)-0.1
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification50000
Calibrated Magnification50000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging DetailsLOW DOSE MODE
EM Software
TaskSoftware PackageVersion
MODEL FITTINGFlex-EM
MODEL FITTINGMODELLER
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONIMAGIC5
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING, FULL CTF CORRECTION