This protein is part of the mitochondrial ribosome of yeast Saccharomyces cerevisiae 1 and consists of 2206 atoms of which 1126 are hydrogen atoms that were added after modeling. The corresponding density map (b6m_density_map.mrc
) and the derived local resolution (b6m_local_resolution.mrc
) have dimensions of 60 x 60 x 60 voxels.
bS6m.pdb
- the initial modelbS6m_bad.pdb
- refined model obtained through automated fitting to the density mapbS6m_refined.pdb
- deteriorated model with approx. 1/3 of the atoms' positions modified
*.resmetrics.csv
- per-residue validation metrics*.clashes.csv
- aggregated atom clash scores (max score per atom)*.clashes-full.txt
- all pair-wise clashes between atoms
This spinach chloroplast ribosome (PDB-ID: 6ERI, EM Map: EMD-3941}) is involved in oxygenic photosynthesis 2. The structure was obtained at 3Å resolution and comprises 145000 atoms distributed over 11094 residues. For some of the chains, including about 5000 residues, we were not able to produce any validation metrics as those are marked as ``unknown''.
6eri.cif
- atomic structure of 6ERIemd_3941.map
- density map (not included), accessible via the Electron Microscopy Data Bank EMD-3941emd_3941_resmap.map
- local resolution derived from the density map and its halfmaps
6eri.resmetrics.csv
- per-residue validation metrics6eri.clashes.csv
- aggregated atom clash scores (max score per atom)6eri.clashes-full.txt
- all pair-wise clashes between atoms
Footnotes
-
N. Desai, A. Brown, A. Amunts, and V. Ramakrishnan, "The structure of the yeast mitochondrial ribosome," Science, vol. 355, no. 6324, pp. 528–531, 2017. ↩
-
A. P. Boerema, S. Aibara, B. Paul, V. Tobiasson, D. Kimanius, B. O. Forsberg, K. Wallden, E. Lindahl, and A. Amunts, "Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor," Nature plants, vol. 4, no. 4, pp. 12–217, 2018. ↩