8D2V
Zebrafish MFSD2A isoform B in inward open ligand 1B conformation
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7MJS |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.54 |
f_angle_d | 0.74 |
f_chiral_restr | 0.047 |
f_plane_restr | 0.007 |
f_bond_d | 0.004 |
Sample |
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Single-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 1B conformation at an average resolution of 4.1 A, filtered to local resolution |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details | 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 ... |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 413435 |
Reported Resolution (Å) | 4.1 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 (7MJS) | 2 (7MJS) | |||
Refinement Space | REAL | REAL | |||
Refinement Protocol | RIGID BODY FIT | FLEXIBLE FIT | |||
Refinement Target | |||||
Overall B Value | 220 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS KRIOS |
Minimum Defocus (nm) | 500 |
Maximum Defocus (nm) | 1800 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 0.01 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 81000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Cryo-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 | ||
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Task | Software Package | Version |
MODEL FITTING | UCSF Chimera | |
IMAGE ACQUISITION | SerialEM | |
INITIAL EULER ASSIGNMENT | cryoSPARC | v3.3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | v3.3.2 |
CLASSIFICATION | cryoSPARC | v3.3.2 |
RECONSTRUCTION | cryoSPARC | v3.3.2 |
MODEL FITTING | Coot | |
MODEL REFINEMENT | Coot | |
MODEL REFINEMENT | PHENIX | |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |