Breaking good resolutions with ARP/wARP

Abstract

New procedures are outlined that enable ARP/wARP to automatically build protein models with diffraction data extending to about 2.5 Å. An overview of ongoing research is given and possible future advances are discussed.

Structural and Molecular Characterization of Iron-sensing Hemerythrin-like Domain within F-box and Leucine-rich Repeat Protein 5 (FBXL5)

“…Phases were further improved by density modification and 2-fold noncrystallographic averaging with the program DM (24), resulting in a figure of merit of 0.85. An initial model containing about 86% of all residues was automatically generated by alternating cycles of the programs ARP/warp (25). Additional residues were manually modeled in the program O (26).…”

The 1.58 Å resolution structure of the DNA-binding domain of bacteriophage SF6 small terminase provides new hints on DNA binding

“…The initial phases were extended to 1.58 Å resolution with DM (Cowtan, 2010) using the native data set and keeping 5% of the reflections as an R free set. ARP/ wARP (Morris et al, 2004) was used to automatically build a model that was $93% complete. The missing residues located at the N-terminus were added manually using Coot (Emsley et al, 2010).…”

Crystallization and preliminary X-ray analysis of 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase fromArthrobacter nitroguajacolicusRü61a: a cofactor-devoid dioxygenase of the α/β-hydrolase-fold superfamily

“…A clear difference in contrast was seen between the original and inverted-hand enantiomorphs. Inspection of the electron-density maps revealed regions of correct right-hand helices in space group P4 3 2 1 2 which could be fitted to helical segments using the ARP/wARP HelixBuild module (Morris et al, 2004). Model building using maps calculated from SHARP (Bricogne et al, 2003) improved phases is nearly complete.…”