4CKD
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) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1F4A | |
| Sample |
|---|
| SINGLE CHAIN FV ANTIBODY DOMAIN BOUND TO THE ENZYME BETA-GALACTOSIDASE |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 100, INSTRUMENT- OTHER, METHOD- BLOT FOR 10-20 SECONDS UNTIL DIAMETER OF BLOTTED MENIS ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 2965 |
| Reported Resolution (Å) | 13 |
| Resolution Method | |
| Other Details | 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 RESOL ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1F4A) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | FSC CURVE BETWEEN MAP AND MODEL | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 67 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2012-08-02 |
| Temperature (Kelvin) | 89 |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 2678 |
| Maximum Defocus (nm) | 4027 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 59000 |
| Calibrated Magnification | 81600 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | EXPOSURE 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 | ||
|---|---|---|
| Task | Software Package | Version |
| CTF CORRECTION | CTFFIND | 3 |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | FREALIGN | |
| RECONSTRUCTION | MRC IMAGE PROCESSING PACKAGE | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| DONE INSIDE FREALIGN | ||||
