Computational protocol: Crystal structures of ternary complexes of archaeal B-family DNA polymerases

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Protocol publication

[…] Data for the project was collected at the beamlines PXI and PXIII at the Swiss Light Source (SLS), Paul-Scherrer Institute, Villigen, Switzerland. Data reduction was performed with the XDS package [] and structures were solved by molecular replacement with PHENIX using the binary KOD exo- [] and binary 9°N exo- [] structures. Refinement was performed with PHENIX [] and model rebuilding was done with COOT.[] In iterative rounds of refinement and model building geometry was validated using the MolProbity Server.[, ] In the KOD and 9°N models the C-terminal amino acids were not modelled due to missing electron density. Side chains with weak electron density were not deleted but modelled in a common rotamer conformation and high B-factors demonstrate their flexibility. The restraint file for the ligand DTP was generated using the Grade webserver.[] Figures were generated with PyMOL.[] The figures showing the inner channels of the DNA pols () were generated using Chimera.[] For comparison of enzymes, the complete complexes were superposed in PyMOL. To determine rmsd values only Cα atoms were superposed in PyMOL with the default values (e.g. outlier rejection cutoff in RMS = 2, outlier rejection cycles = 5). Data collection and refinement statistics are summarized in . […]

Pipeline specifications

Software tools XDS, PHENIX, Coot, MolProbity, PyMOL
Applications Small-angle scattering, Protein structure analysis
Chemicals Nucleotides