3JD5 | pdb_00003jd5

Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AJ3
experimental model	PDB	3J9M

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.401
f_angle_d	0.304
f_chiral_restr	0.028
f_plane_restr	0.003
f_bond_d	0.001

Sample
small subunit of mitochondrial ribosome

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	Plunged into liquid ethane (FEI VITROBOT MARK I).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	307556
Reported Resolution (Å)	7
Resolution Method
Other Details	A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classi ...	A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classification, ~28% of the particles - those with low cross-correlation coefficient values with the 55S reference projections - were removed.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5AJ3, 3J9M)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	METHOD--Flexible fitting REFINEMENT PROTOCOL--rigid body

Data Acquisition
Detector Type	GATAN ULTRASCAN 1000 (2k x 2k)
Electron Dose (electrons/Å**2)	9

Imaging Experiment	1
Date of Experiment	2009-10-10
Temperature (Kelvin)	100
Microscope Model	JEOL 3200FS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	60000
Calibrated Magnification	59717
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
RECONSTRUCTION	RELION	1.2
RECONSTRUCTION	SPIDER
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTFFIND3

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 R01GM157729.