4AB3
ATP-triggered molecular mechanics of the chaperonin GroEL
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1OEL |
Sample |
---|
GROEL-ATP14 RD5-RDOPEN |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK I |
Cryogen Name | ETHANE |
Sample Vitrification Details | VITRIFIED WITH A VITROBOT AT 100 PERCENT HUMIDITY WITH 2-3 SECONDS BLOTTING TIME |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 15000 |
Reported Resolution (Å) | 8.5 |
Resolution Method | |
Other Details | SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2003.(DEPOSITION ID: 10412). |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | D7 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (1OEL) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | METHOD--FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 15 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | 95 |
Microscope Model | FEI TECNAI F20 |
Minimum Defocus (nm) | 700 |
Maximum Defocus (nm) | 3500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | 148500 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 120 |
Imaging Details | THE DATA WERE COLLECTED WITH LEGINON AT SCRIPPS |
EM Software | ||
---|---|---|
Task | Software Package | Version |
MODEL FITTING | Flex-EM | |
MODEL FITTING | NAMD | 2.6 |
MODEL FITTING | UCSF Chimera | |
RECONSTRUCTION | IMAGIC | |
RECONSTRUCTION | SPIDER |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
EACH PARTICLE WAS PHASE FLIPPED |