8P7X | pdb_00008p7x

Mycoplasma pneumoniae 70S ribosome in chloramphenicol-treated cells

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OOC
experimental model	PDB	7OOD

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.01
f_angle_d	0.591
f_chiral_restr	0.031
f_plane_restr	0.006
f_bond_d	0.003

Sample
Mycoplasma pneumoniae M129 cells treated with chloramphenicol

Specimen Preparation
Sample Aggregation State	CELL
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details	Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental control chamber

3D Reconstruction
Reconstruction Method	SUBTOMOGRAM AVERAGING
Number of Particles	30774
Reported Resolution (Å)	3.03
Resolution Method	FSC 0.143 CUT-OFF
Other Details	half maps from Warp/M
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7OOC, 7OOD)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	All models were refined over multiple rounds using the module phenix.real_space_refine in PHENIX and interactive model building and refinement in Coot ...	All models were refined over multiple rounds using the module phenix.real_space_refine in PHENIX and interactive model building and refinement in Coot, using libG restraints for the RNA.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	3.34

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3250
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	64000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
VOLUME SELECTION	PyTom	0.9.7.1
VOLUME SELECTION	Warp	1.0.9
IMAGE ACQUISITION	SerialEM	3.9
CTF CORRECTION	Warp	1.0.9
MODEL FITTING	Coot	0.9.8.5
MODEL FITTING	LIBG	ccp4-8.0
FINAL EULER ASSIGNMENT	RELION	3.0.8
FINAL EULER ASSIGNMENT	Warp	1.0.9
CLASSIFICATION	RELION	3.0.8
RECONSTRUCTION	Warp	1.0.9
MODEL REFINEMENT	PHENIX	1.20.1_4487

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF estimation and 3D CTF correction are done in Warp