Computational protocol: Crystal structure of Qa-1a with bound Qa-1 determinant modifier peptide

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Protocol publication

[…] Diffraction data for Qa-1a/β2m/Qdm crystal were processed and scaled using HKL2000. The Qa-1a/β2m/Qdm structure was solved by molecular replacement method using the protein coordinates from structure of Qa-1b/β2m/Qdm (PDB ID 3VJ6, with Qdm peptide removed) using PHASER [] as part of the CCP4 suite []. The model was built and refined iteratively using COOT [] and REFMAC5 [], and monitored by a continuous drop in Rfree values and improvement in electron density. Refinement was carried out to a final Rcryst and Rfree of 21.8% and 24.5%. Data collection and refinement statistics are presented in . [...] The quality of the models were examined using Molprobity [].Buried surface areas (BSA) and atomic contacts were calculated using PDBePISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html). Figures were prepared using PyMOL (Schroedinger). […]

Pipeline specifications

Software tools CCP4, Coot, REFMAC5, MolProbity, PyMOL
Application Protein structure analysis
Chemicals Amino Acids