Computational protocol: The double PHD finger domain of MOZ/MYST3 induces α-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification

Similar protocols

Protocol publication

[…] After density modification, model building of the MOZ DPF–H3 complex structure was straight forward and was performed using a combination of automatic model building (RESOLVE) and manual rebuilding and adjustments in COOT (). The structure was refined to a final crystallographic Rfactor of 16.5% and Rfree of 18.6% using the PHENIX suite of programs (). Ninety-eight percent of residues were in the favoured regions of the Ramachandran plot and 2% in the allowed regions. The DPF in complex with H3K9ac was refined to an Rfactor of 16.5% and Rfree of 18.5%, with 98% of residues in the preferred and 2% of residues in the allowed regions of the Ramachandran plot. The unbound MOZ DPF crystal structure was refined to a final Rfactor of 23.9% and Rfree of 25.5%, respectively. Ninety-five percent of residues were in preferred regions and 5% of residues in the allowed regions. In this structure, residues 270–273 were poorly defined in the electron density and therefore not modelled. MOZ DPF in complex with H3K14ac was refined to a final Rfactor of 21.9% and Rfree of 26.6%. In the final model, 95% of residues were in the preferred regions and 5% of residues were in the allowed regions of the Ramachandran plot. All steps of refinement were carried out using the PHENIX suite using a maximum likelihood target and non-crystallographic symmetry (NCS) restraints where applicable (). After each round of refinement electron density maps were inspected visually and the models manually adjusted in COOT (). The geometry and overall quality of the structures was assessed using MOLPROBITY (). […]

Pipeline specifications

Software tools Coot, PHENIX, MolProbity
Application Protein structure analysis
Chemicals Glycine