Home EMD-2182 Mirrors RCSB (USA) EBI (UK)  Contact EMDataBank

Title: Electron microscopy map of SOS1 antiporter Authors: Nunez Ramirez R, Sanchez Barrena MJ, Villalta I, Vega JF, Pardo JM, Quintero FJ, Martinez Salazar J, Albert A Sample: Antiporter SOS1 Method: Single particle reconstruction (25.9 angstroms resolution) Latest update: 2012-11-28   Summary  Experimental details   Visualization   Map information   Downloads Sample Sample name: Antiporter SOS1 Oligomeric state: Dimer Theoretical molecular weight of the sample: 0.254 Components: ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details 1 protein Na+/H+ antiporter SOS1 Dimer true Arabidopsis thaliana Experiment Specimen state: Particle Specimen preparation: pH Specimen conc. Details Staining Specimen support details 8.5 mg/mL 50 mM phosphate buffer pH 8.5, 300 mM NaCl, 10% glycerol, 0.05% DDM, 250 mM imidazole Purified SOS1 was adsorbed to glow-discharged carbon coated grids and stained with 2% uranyl formate 400 mesh carbon coated copper grid, glow discharged in moderate vacuum Vitrification: Cryogen name Humidity Temp. Instr. Method Time resolved Details NONE % K NONE ms Imaging: Microscope Voltage Illumination mode Imaging mode Cs Defocus min. Defocus max. Nominal mag. Calibrated mag. Electron source Detector Detector distance Astigmatism JEOL 2100 200 kV FLOOD BEAM BRIGHT FIELD 1.0 mm 1000 nm 2500 nm 20000 20000 LAB6 Orius Gatan CCD camera mm Objective lens astigmatism was corrected at 120.000-150.000 times magnification and confirmed by inspection of the Fourier transform Specimen holder Holder model Tilt min. Tilt max. Energy filter Energy window Temp. Temp. min. Temp. max. Beam tilt Electron dose Other details Date JEOL 0° 0° eV K K K mrad 15 e/Å2 01-NOV-2010 Processing Protocol: 3D maximum likelihood Software: XMIPP CTF correction: Each micrograph. Estimation using CTFFIND3 and correction using Bsoft Number of particles: 6300 Number of class averages: 96 Resolution by author: 25.9 Å Resolution method: FSC at 0.5 cut-off Processing details: Single images of SOS1 were manually extracted using EMAN. 2D reference-free classification, 2D averaging, 3D classification and reconstruction were performed using maximum-likelihood methods implemented in XMIPP package. Scanned images: Num. images Sampling size OD range Quant. bit number Other details Scanner 90 μm/pixel 14 Fitting: PDB Protocol Target crit. Software B value Fitting space PDB chain Details