Computational protocol: Crystal Structure of a p53 Core Tetramer Bound to DNA

Similar protocols

Protocol publication

[…] Crystals were grown in 200 mM lithium citrate, 20% PEG 3350 by hanging drop vapor diffusion. Small, rectangular crystals appeared in two days and reached a maximum size of 160 × 30 × 30 uM after one week. Crystals were frozen in the well condition with 15 – 20% glycerol. Data collection was carried out on the 23-IDB beamline at the Advanced Photon Source synchrotron at Argonne National Laboratories. Data was indexed and scaled using HKL2000 (). The structures were solved by molecular replacement using PHASER with 2GEQ as a search model. For structure 1, the resulting solution was the p53DBD dimer bound to its half site in an asymmetric unit cell with a full tetramer containing a crystallographic two-fold axis. For structure 2, the resulting solution was the p53DBD monomer bound to its quarter site in an asymmetric unit. These models were refined in CNS using simulated annealing, minimization and individual B-factor refinement. For structure 1, medium NCS restraints were initially used for the two p53DBD domains in the asymmetric unit. The NCS restraints were gradually lowered and were eventually dropped completely. Between refinement cycles, the model was manually rebuilt using the program Coot(). Data collection and refinement statistics for structures 1 and 2 are summarized in . […]

Pipeline specifications

Software tools CNS, Coot
Application Protein structure analysis
Organisms Dipturus trachyderma, Homo sapiens