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 4CKD | pdb_00004ckd

Model of complex between the E.coli enzyme beta-galactosidase and four single chain Fv antibody domains scFv13R4.


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F4A 
Sample
SINGLE CHAIN FV ANTIBODY DOMAIN BOUND TO THE ENZYME BETA-GALACTOSIDASE
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 100, INSTRUMENT- OTHER, METHOD- BLOT FOR 10-20 SECONDS UNTIL DIAMETER OF BLOTTED MENIS ...VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 100, INSTRUMENT- OTHER, METHOD- BLOT FOR 10-20 SECONDS UNTIL DIAMETER OF BLOTTED MENISCUS CEASES TO EXPAND, BEFORE PLUNGING.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles2965
Reported Resolution (Å)13
Resolution Method
Other DetailsFREALIGN MAP OBTAINED FROM 2965 PARTICLES USING D2 SYMMETRY THIS IS A MODEL MADE BY DOCKING TWO ATOMIC MODELS AS RIGID BODIES INTO A 13 ANGSTROM RESOL ...FREALIGN MAP OBTAINED FROM 2965 PARTICLES USING D2 SYMMETRY THIS IS A MODEL MADE BY DOCKING TWO ATOMIC MODELS AS RIGID BODIES INTO A 13 ANGSTROM RESOLUTION DENSITY MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2548. (DEPOSITION ID: 12230).
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1 (1F4A)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetFSC CURVE BETWEEN MAP AND MODEL
Overall B Value
Fitting Procedure
DetailsMETHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)67
Imaging Experiment1
Date of Experiment2012-08-02
Temperature (Kelvin)89
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)2678
Maximum Defocus (nm)4027
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification59000
Calibrated Magnification81600
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsEXPOSURE INTENSITY SET TO GIVE 50 ELECTRONS PER PIXEL PER SECOND AT THE DETECTOR. THIS TRANSLATES INTO 16 ELECTRONS PER SQUARE ANGSTROM PER SECOND AT THE SPECIMEN.
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONCTFFIND3
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONMRC IMAGE PROCESSING PACKAGE
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
DONE INSIDE FREALIGN