Table 2.
Data collection and structure determination statistics. Crystallographic parameters, data-collection (native data) and refinement statistics for Archaeoglobus fulgidus and Nitrosomonas europaea proteins (apo and ligand-bound structures)
| apo-AF0826 3DLO | AF0826-dAMP 3QTB | apo-NE1028 2PFS | NE1028-AMP 3TNJ | |
|---|---|---|---|---|
| Data collection | ||||
| Beamline | 19-BM | 21-ID | 19-ID | 19-BM |
| Wavelength (Å) | 0.9793 | 0.9792 | 0.9792 | 0.9791 |
| Resolution (Å) | 1.97 (1.97–2.03) | 2.10 (2.10–2.14) | 2.25 (2.25–2.29) | 2.00 (2.00–2.03) |
| Space group | P21 | C2 | P321 | P321 |
| a (Å)/b (Å) | 43.2/99.2 | 109.6/42.7 | 76.0/77.8 | 77.8/77.8 |
| c (Å) | 57.4 | 61.3 | 43.0 | 39.9 |
| α/β (°) | 90.0/92.4 | 90.0/116.8 | 90.0/90.0 | 90.0/90.0 |
| γ (°) | 90.0 | 90.0 | 120.0 | 120.0 |
| Solvent content (%) | 30.7 | 33.3 | 42.5 | 41.5 |
| Completeness (%) | 99.6 (77.6) | 99.6 (98.8) | 97.60 (81.5) | 97.5 (93.7) |
| Observed reflections | 33270 | 36964 | 6882 | 9070 |
| Unique reflections | 33213 | 33270 | 6538 | 8637 |
| I/σ (I) | 24.1 (2.7) | 21.5 (2.6) | 58.5 (2.9) | 29.0 (2.7) |
| Rmerge (%) | 7.3 (40.5) | 7.0 (40.5) | 6.0 (48.6) | 5.1 (57.5) |
| Refinement | ||||
| R (%)/Rmerge (%) | 17.5/23.0 | 20.0/23.7 | 19.8/25.5 | 19.1/24.1 |
| Mean B values (Å2) | 23.2 | 38.9 | 52.4 | 48.8 |
| Protein atoms | 4398 | 1970 | 944 | 996 |
| Chloride ions | 2 | 0 | 2 | 0 |
| Water molecules | 182 | 50 | 40 | 36 |
| Structure quality | ||||
| Ramachandran statistics* | ||||
| Favored (%)/n | 97.9 | 99.6 | 100 | 100 |
| Allowed (%)/n | 2.1 | 0.4 | 0 | 0 |
| All-atoms contacts and protein geometry | ||||
| Clash score | 12.25 (71st)† | 8.15 (93rd)† | 9.17 (93rd)† | 7.47 (93rd)† |
| MolProbity score | 2.13 (63rd)† | 1.44 (99rd†) | 1.85 (93rd)† | 1.61 (94rd)† |
| RMS deviation | ||||
| Bond lengths (Å) | 0.019 | 0.013 | 0.017 | 0.014 |
| Bons angles (°) | 1.8 | 1.5 | 1.6 | 1.4 |
Data for the highest resolution shell are given in parentheses.
*
Pro and Gly residues were excluded from calculation.
*
Percentile.