Computational protocol: Crystal Structure of Two Anti-Porphyrin Antibodies with Peroxidase Activity

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Protocol publication

[…] Diffraction data for Fab 13G10 and Fab 14H7 were recorded at the ID14-1 station of ESRF and the LURE DW32 station, respectively. Data were processed with DENZO and SCALEPACK (). The structures were solved by molecular replacement with the program AMoRe ; the models used were the Fv domain (PDB code 1mfa) and the CL-CH1 dimer (PDB code 1mfe) of the murine anticarbohydrate antibody Se155-4, which belongs to the same IgG1, λ class . The atomic model of 13G10 was refined alternating cycles of model reconstruction with O and refinement with CNS , whereas the atomic model of 14H7 was refined alternating cycles of model reconstruction with COOT and refinement with PHENIX using the twin option. The final refinement statistics are given in . Several residues at the N-terminus of the heavy chain and CDRH1 of four heavy chains that were disordered were not included in the model. Figures were drawn with PYMOL. ThrL51 in CDRL2, which lies in the disallowed region of the Ramachandran plot, belongs to a γ turn, as commonly observed in all antibody structures. […]

Pipeline specifications

Software tools CNS, Coot, PHENIX, PyMOL
Application Protein structure analysis
Chemicals Amino Acids, Hydrogen, Iron