9SSC | pdb_00009ssc

Cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimeric assembly

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9SRQ

Sample
Homotrimer of the essential Mycoplasma pneumoniae lipoprotein Mpn444

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Nominal blot force -3 Wait time 10 s Blotting time 14 s. Before freezing, Whatman 595 filter papers were incubated for 1 h in the Vitrobot chamber at 100% relative humidity and 278K.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	506291
Reported Resolution (Å)	5.85
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (9SRQ)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	3600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v4.5.3
IMAGE ACQUISITION	SerialEM	v4.1.0 beta
CTF CORRECTION	cryoSPARC	v4.5.3
MODEL FITTING	UCSF ChimeraX
INITIAL EULER ASSIGNMENT	cryoSPARC	v4.5.3
FINAL EULER ASSIGNMENT	cryoSPARC	v4.5.3
CLASSIFICATION	cryoSPARC	v4.5.3
RECONSTRUCTION	cryoSPARC	v4.5.3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		6832694