Computational protocol: Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes

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Protocol publication

[…] The protein crystallized in several conditions of the Crystal Screen HT (Hampton Research). After optimization, Mdv1-CCSeMet (10 mg/ml in 20 mM Tris-Cl, pH 7.5, and 100 mM NaCl) was crystallized in 2 µl/2 µl vapor diffusion experiments against a well solution containing 16% PEG 3350, 0.1 M Bis-Tris-Propane, pH 7.5, and 0.4 M NaCl. Flat-plate crystals were cryoprotected in 20% PEG 3350, 0.1 M BTP, pH 7.5, 0.4 M NaCl, and 25% glycerol and flash frozen in liquid nitrogen. Peak and inflection data were collected on beamline (version 7.1; SSRL) and processed with HKL2000 () to a final Rmerge of 5.3% to 2.6 Å. The selenium sites were identified with SOLVE (), and solvent flattening and preliminary model building with RESOLVE () resulted in 60% of the residues correctly positioned. Final model building and validation was performed in COOT (). Refinement with REFMAC5 () within the CCP4 suite () resulted in a final Rfactor/Rmerge of 27.1%/31.1% and a model with good geometric statistics (Table S2). […]

Pipeline specifications

Software tools Coot, REFMAC5, CCP4
Application Protein structure analysis
Organisms Saccharomyces cerevisiae, Gallid alphaherpesvirus 2