9NFK | pdb_00009nfk

Tuna P-glycoprotein Apo Conformation 3


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
ABC transporter from yellowfin tuna
Specimen Preparation
Sample Aggregation State2D ARRAY
Vitrification InstrumentSPT LABTECH CHAMELEON
Cryogen NameETHANE
Sample Vitrification DetailsThe grids were glow discharged for 80sec at 12mA, with a relative humidity of 82% and temperature 21.5oC maintained throughout preparation. Samples of ...The grids were glow discharged for 80sec at 12mA, with a relative humidity of 82% and temperature 21.5oC maintained throughout preparation. Samples of purified protein were concentrated to 1mg/mL and ultracentrifuged in a Beckmann Optima Ultracentrifuge for 15 minutes prior to grid preparation. The sample was applied via 2-S application mode by the Chameleon, allowed to wick for 530ms via the grid nanowires, and subsequently plunged into liquid ethane maintained at -180oC.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles75691
Reported Resolution (Å)3.99
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value97
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)55
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv4.5.3
IMAGE ACQUISITIONcryoSPARCv4.5.3
CTF CORRECTIONcryoSPARCv4.5.3
MODEL FITTINGPHENIX1.21.1_5286
MODEL REFINEMENTPHENIX1.21.1_5286
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION4800000