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) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3STJ | |
| Sample |
|---|
| ESCHERICHIA COLI DEGQ 12- MER IN COMPLEX WITH A BINDING PEPTIDE |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING, |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 29432 |
| Reported Resolution (Å) | 7.5 |
| Resolution Method | |
| Other Details | 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 UNKNOW ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3STJ) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--RIGID BODY AND FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 15 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | 91 |
| Microscope Model | FEI TECNAI F20 |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | -0.1 |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 50000 |
| Calibrated Magnification | 50000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details | LOW DOSE MODE |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Flex-EM | |
| MODEL FITTING | MODELLER | |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | IMAGIC | 5 |
| RECONSTRUCTION | SPIDER | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING, FULL CTF CORRECTION | ||||
