Experiment: 6YSI

Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MDZ
experimental model	PDB	5AFI

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.166
f_angle_d	0.7298
f_chiral_restr	0.045
f_bond_d	0.0079
f_plane_restr	0.0053

Sample
Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit

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)	2.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Multi-body refinement was carried out in RELION 3.0 to obtain the final '50S subunit' reconstruction. The mask used for this procedure is deposited wi ...	Multi-body refinement was carried out in RELION 3.0 to obtain the final '50S subunit' 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 (5MDZ, 5AFI)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	correlation coefficient
Overall B Value
Fitting Procedure
Details

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
MODEL REFINEMENT	PHENIX	1.17.1-3660
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.0
RECONSTRUCTION	RELION	3.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION