6YTF

ELECTRON MICROSCOPY

Sample

Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument ?
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 231159
Reported Resolution (Å) 3.0
Resolution Method FSC 0.143 CUT-OFF
Other Details Multi-body refinement was carried out in RELION 3.0 to obtain the final '30S subunit head' reconstruction. The mask used for this procedure is deposited with this entry.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details The quality of the map is relatively poor so the related PDB entry 6YS5 (A. baumannii ribosome-amikacin complex - 30S subunit head) was rigid body fitted into the map using Chimera X-0.9, tigecycline was placed into the density at the primary site, and one round of global real space refinement and local refinement were carried out using PHENIX and Coot respectively, using ligand restraints in both cases.
Data Acquisition
Detector Type FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å2) 62
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 2600
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 75000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
CTF CORRECTION Gctf 1.18
MODEL FITTING UCSF Chimera X-0.9
INITIAL EULER ASSIGNMENT RELION 3.0
FINAL EULER ASSIGNMENT RELION 3.0
RECONSTRUCTION RELION 3.0
MODEL REFINEMENT PHENIX 1.17.1-3660
MODEL REFINEMENT Coot 0.8.9.2
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?