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 8D2S | pdb_00008d2s

Zebrafish MFSD2A isoform B in inward open ligand bound conformation


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7MJS 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.756
f_angle_d0.653
f_chiral_restr0.043
f_plane_restr0.006
f_bond_d0.003
Sample
Single-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand bound conformation at an average resolution of 2.9 A, filtered to local resolution
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details400-mesh 1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for two times 60 seconds with a current of 15 mA in a PELCO easiGlow ...400-mesh 1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for two times 60 seconds with a current of 15 mA in a PELCO easiGlow system. The cryo grids were produced using a Leica EM GP (Leica). The chamber was kept at 4 C and 95% humidity (86-91% measured). 3 microliter sample at 3 mg/ml was applied to a glow-discharged holey grid, blotted for 6 s, and plunge frozen into liquid ethane and stored in liquid nitrogen.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles295580
Reported Resolution (Å)2.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7MJS)2 (7MJS)
Refinement SpaceREALREAL
Refinement ProtocolRIGID BODY FITFLEXIBLE FIT
Refinement Target
Overall B Value123
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.01
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsCryo-EM grids were loaded into a 300 keV FEI Titan Krios cryo electron microscope (ThermoFisher Scientific, formerly FEI) at HHMI Janelia Reasearch Campus, Janelia Krios 1, equipped with a Cs corrector, and Gatan energy filter and K3 camera (Gatan Inc.). Movies of 50 frames with 1 e-/A2 per frame (50 e-/A2 total dose) were automatically recorded at a nominal magnification of 81,000x, corresponding to a physical pixel size of 0.844 A/px (superresolution pixel size 0.422 A/px) in CDS mode at a dose rate of 9.5 e-/px/s (~7.5 e-/px/s on the camera through the sample) and a defocus range of -0.5 to -1.8 micrometer using SerialEM. In total, 2,653 and 8,443 movies were collected in two separate imaging sessions, with the first dataset on a 400-mesh copper grid and the second on a 300-mesh UltrAuFoil gold grid.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1.2
MODEL FITTINGUCSF Chimera
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctf1.18
MODEL FITTINGCoot
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTRELION3.1.2
INITIAL EULER ASSIGNMENTcryoSPARCv3.3.2
FINAL EULER ASSIGNMENTcryoSPARCv3.3.2
CLASSIFICATIONcryoSPARCv3.3.2
RECONSTRUCTIONcryoSPARCv3.3.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONPatch CTF3657332Good 2D classes generated from ~1,000 manually picked particles served as templates for automatic particle picking in RELION, resulting in 623,644 and 3,033,688 particles in dataset 1 and dataset 2 respectively