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 9SRV | pdb_00009srv

Partial cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn436 (flexible loops excluded)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Essential Mycoplasma pneumoniae lipoprotein Mpn436
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsNominal blot force -3 Wait time 10 s Blotting time 8-14 s. Before freezing, Whatman 595 filter papers were incubated for 1 h in the Vitrobot chamber ...Nominal blot force -3 Wait time 10 s Blotting time 8-14 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 MethodSINGLE PARTICLE
Number of Particles468211
Reported Resolution (Å)3.65
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)3600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv4.5.3
IMAGE ACQUISITIONSerialEMv4.1.0 beta
CTF CORRECTIONcryoSPARCv4.5.3
MODEL FITTINGISOLDE
INITIAL EULER ASSIGNMENTcryoSPARCv4.5.3
FINAL EULER ASSIGNMENTcryoSPARCv4.5.3
CLASSIFICATIONcryoSPARCv4.5.3
RECONSTRUCTIONcryoSPARCv4.5.3
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION6582748