8CSP | pdb_00008csp

Human mitochondrial small subunit assembly intermediate (State A)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RW4
experimental model	PDB	2C2N
experimental model	PDB	6AAX

Sample
Human mitochondrial small subunit assembly intermediate, State A

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	263184
Reported Resolution (Å)	2.66
Resolution Method	FSC 0.143 CUT-OFF
Other Details	12 focused maps calculated in RELION 3.1.1 were combined into a composite map using phenix.combine_focused_maps. Composite half maps were generated by ...	12 focused maps calculated in RELION 3.1.1 were combined into a composite map using phenix.combine_focused_maps. Composite half maps were generated by combining each half map from focused refinements.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6RW4, 2C2N, 6AAX)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	51

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
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
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf	1.18
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot	0.9.5
MODEL REFINEMENT	PHENIX	1.19
INITIAL EULER ASSIGNMENT	RELION	3.1.1
FINAL EULER ASSIGNMENT	RELION	3.1.1
CLASSIFICATION	RELION	3.1.1
RECONSTRUCTION	PHENIX	1.19

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		9109335

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.