PcaA• Mycolic acid cyclopropyl synthase

(Smith&Sacchettini)• original structure solved at 2.0A via MAD

R-value = 0.22, R-free = 0.27

• 287 residues, fold

Example of density quality (~1 contour with C trace)

Electron density map (2.8A)

Results of tracing

Strip off branches of trace (linearize)

Linearized trace shows backbone connectivity

Pick C’s using neural net; link together

Results of CAPRA

Comparison to backbone of true structure (white)

Percent built = 89% (missing: 15-residue N-terminus, 17-residue disordered loop)4 single-atom insertions; 5 single-atom deletionsRMSD = 0.81A

CAPRA model consists of 3 chains

Chain lengths: 14, 96, 145 residues

Results of LOOKUP (modeling side-chains)

Comparison of TEXTAL model to true structure

Percent amino acid identity = 87.5% (mistakes: small frame-shifts around gaps in alignment)all-atom RMSD = 0.92A

Closeup of -strand (TEXTAL model in green)

Closeup of -helix (TEXTAL model in green)

If5A• Translation initiation factor 5A (Peat&Terwilliger)• 136 residues, -fold• original structure solved at 1.75A by MAD

R-value = 0.21, R-free = 0.24

Example of density quality(~1 contour with C trace)

Electron density map (2.8A) with C chains generated by CAPRA

(CAPRA chains shown in color; true backbone shown in white)

Results of CAPRA

Percent built = 94%chain lengths: 16, 20, 44, 57C RMSD = 0.76A

LOOKUP: fitting side-chains into density

Results of LOOKUP, comparison to true structure

Percent identity = 84% all-atom RMSD = 0.92A

(TEXTAL model in green; true structure in red/white/blue)

Focus on backbone atoms

Notice accuracy of carbonyl oxygens and chain directionality

Closeup of a strand within a -sheet

Closeup of another -strand and turn