6N1P
Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2 symmetry
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4Z2C |
Sample |
---|
Complex of DNA Gyrase A subunit with DNA in C2 symmetry |
Sample Components |
DNA Gyrase A |
DNA |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 30637 |
Reported Resolution (Å) | 6.35 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (4Z2C) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 62 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | JEOL 3200FS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 3000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Nominal Magnification | 30000 |
Calibrated Magnification | 40323 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | 2.1 |
IMAGE ACQUISITION | Leginon | 3.2 |
CTF CORRECTION | CTFFIND | 4.1 |
MODEL FITTING | MDFF | 0.4 |
INITIAL EULER ASSIGNMENT | RELION | 1.4 |
FINAL EULER ASSIGNMENT | RELION | 2.1 |
CLASSIFICATION | RELION | 2.1 |
RECONSTRUCTION | RELION | 2.1 |
MODEL REFINEMENT | REFMAC | 5 |
MODEL REFINEMENT | PHENIX | 1.12-2829 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 387297 |