6YTF

Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.6587
f_angle_d	0.8528
f_chiral_restr	0.0485
f_bond_d	0.0071
f_plane_restr	0.0059

Sample
Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head

Specimen Preparation
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
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 deposit ...	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
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6YS5, 5AFI)
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 fit ...	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/Å**2)	62

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.