Computational protocol: Structural Analysis of the Synthetic Duffy Binding Protein (DBP) Antigen DEKnull Relevant for Plasmodium vivax Malaria Vaccine Design

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Protocol publication

[…] DEKnull crystals were grown by hanging-drop vapor diffusion. First, 1 μL of protein solution at 3–9 mg/mL was mixed with 1 μL of reservoir containing 0.2 M di-sodium tartrate, 20% PEG 3350 to create needle clusters. Crystals were shattered and microseeded into a mix of 1 μL of protein solution at 4 mg/mL and 1 μL of reservoir containing 0.2 M lithium chloride, 20% PEG 3350. Large needle rods of DEKnull grew within a week and were flash frozen in liquid nitrogen. Data was collected to a resolution of 2.1 Å at beamline 4.2.2 of the Advanced light Source, Lawrence Berkeley National Laboratory and processed with XDS []. [...] The DEKnull structure was solved by molecular replacement in PHASER [] using a single Sal1 DBP-II domain from 3RRC as a starting model. Manual rebuilding in COOT [] and refinement in PHENIX led to a final refined model with final R-factor/R-free of 21.77%/25.88% with good geometry as reported by MOLPROBITY [–]. The MOLPROBITY score of 0.81 places this structure in the top 100th percentile of structures 1.85–2.35 Å. 98.22% of residues lie in favored, 1.78% of residues lie in additionally allowed, and 0% lie in disallowed regions of the Ramachandran plot. Atomic coordinates and structure factors have been deposited into the Protein Data Bank with accession code 4YFS. […]

Pipeline specifications

Software tools XDS, Coot, PHENIX, MolProbity
Applications Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma, Plasmodium vivax
Diseases Malaria