Table 2.
Selected parameters of the originally deposited (left column) and re-refined (right column) MBL structures described in the section ‘Potentially incorrect ligands’ Data prepared as for Table 1.
| Protein | NDM-1 | NDM-1 | Legionella gormanii FEZ-1 | |||
|---|---|---|---|---|---|---|
| PDB accession code | 4rl2 | 5o2f | 4exy | 5n0i | 1k07 | 5wck |
| Resolution [Å] | 66.92–2.01 (2.06–2.01) | 66.92–2.01 (2.06–2.01) | 75.82–1.47 (1.51–1.47) | 75.82–1.47 (1.51–1.47) | 50.00–1.65 (1.69–1.65) | 50.00–1.65 (1.69–1.65) |
| No. of reflections refinement/Rfree | 25437/1345 | 25437/1345 | 87106/4592 | 87106/4592 | 55140/6172 | 55140/6172 |
| Completeness [%] | 97.71(92.68) | 97.71(92.68) | 99.62(96.74) | 99.62(96.74) | 97.29 (89.93) | 97.29 (89.93) |
| <Ι/σ> in the highest resolution shell | 2.9 | 2.9 | 3.0 | 3.0 | 19 | 19 |
| R / Rfree [%] | 15.1/18.9 | 13.2/18.2 | 14.0/18.2 | 10.9/14.7 | 17.4/19.8 | 12.3/15.8 |
| Protein molecules in ASU | 2 | 2 | 2 | 2 | 2 | 2 |
| NCS restraints | - | - | - | Local | ||
| ADP parametrization | Isotropic | Isotropic | Isotropic | Anisotropic | Isotropic | Isotropic |
| No. atoms | ||||||
| Protein | 3594 | 3644 | 3506 | 3594 | 4148 | 4153 |
| Ligands | 54 | 87 | 12 | 36 | 72~^ | 78 |
| Water | 438 | 433 | 369 | 568 | 501 | 866 |
| Ramachandran statistics [%] | ||||||
| Favored/outliers | 97.91/0.21 | 98.55/0.00 | 97.21/0.21 | 98.50/0.00 | 95.96/0.66 | 95.98/0.22 |
| R.m.s. deviations from target values | ||||||
| Bond lengths [Å] | 0.011 | 0.011 s | 0.017 | 0.014 | 0.014 | 0.009 |
| Bond angles [°] | 1.23 | 1.45 | 2.10 J | 1.65 | 1.62 | 1.40 |
| Clashscore/percentile | 6.13/95th | 1.77/100th | 4.75/93th | 2.5/99th | 4.69/96th | 1.19/97th |