Computational protocol: Structure of mouse IP-10, a chemokine

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Protocol publication

[…] The structure of mouse IP-10 was solved by maximum-likelihood molecular replacement using the program Phaser (Read, 2001) from the CCP4 program suite (Collaborative Computational Project, Number 4, 1994). The coordinates of one molecule of human IP-10 in a truncated form (residues 9–­65; PDB code 1o7y; Swaminathan et al., 2003) were used to build the initial search model and a clear solution was obtained in space group C2 with four molecules in the asymmetric unit. A stacking arrangement of molecules in the unit cell for this solution was observed in Coot (Emsley & Cowtan, 2004), which yielded no unfavourable intermolecular contacts. Initial cycles of refinement resulted in an R cryst of 36.0% and an R free of 42.9%. Iterative cycles of energy minimization, individual B-factor refinement and simulated annealing were carried out in CNS (Brünger et al., 1998), alternated with model building using Coot (Emsley & Cowtan, 2004). Residues were replaced according to the amino-acid sequence of mouse IP-10. The positions of 81 water molecules were identified from the |F o| − |F c| electron-density maps above 3σ and were checked manually for their interactions with protein atoms. The missing residues at the N- and C-termini were added as their density appeared with progressive refinement. Refinement was stopped when no further improvement in R free was made. The final model has an R cryst of 27.6% and an R free of 30.3%. Crystallographic statistics are given in Table 1. Figures were produced using the programs PyMOL (DeLano Scientific LLC; http://www.pymol.org) and POV-Ray (http://www.povray.org). […]

Pipeline specifications

Software tools CCP4, Coot, CNS, PyMOL
Application Protein structure analysis
Organisms Mus musculus, Homo sapiens