EMD-12893 Experiments and Validation

Drs2p-Cdc50p in the E1 state

Single particle reconstruction
Overview of EMD-12893
Sample name: Binary complex of Drs2p-Cdc50p with the regulatory lipid PI4P
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Fitted atomic model: 7oh4

Map parameters

Recommended contour level: 0.185 (author)
Number of grid points: 256 × 256 × 256
Voxel size: 1.03 × 1.03 × 1.03 Å
Minimum density: -0.759
Maximum density: 1.261
Average density: 0.002
Standard deviation: 0.03

Sample information

Sample name: Binary complex of Drs2p-Cdc50p with the regulatory lipid PI4P
Ligands: (2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate, MAGNESIUM ION, 2-acetamido-2-deoxy-beta-D-glucopyranose, water
Proteins: Binary complex of Drs2p-Cdc50p with the regulatory lipid PI4P, Drs2p, Cdc50p, Probable phospholipid-transporting ATPase DRS2,Probable phospholipid-transporting ATPase DRS2, Cell division control protein 50

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: cryoSPARC
Number of particles: 167226

Fitting

Initial atomic model: 6ROJ
Target criteria: correlation coefficient
Overall B value: 55.0
Refinement space: REAL
Details: Domains were rigid body fit into the density and manually adjusted and reconnected.

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 60.0
Energy filter: GIF Bioquantum
Nominal CS (mm): 2.70
Holder model: OTHER
Acquisition
Number of images: 2074

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 0.60
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100