Table 1.
Structural data collection and refinement statistics
| Data | USPSa-CDA | Se-USPSa-CDA |
|---|---|---|
| Protein Data Bank ID | 7JI4 | |
| Data collection | ||
| Space group | P43212 | P43212 |
| Cell dimensions | ||
| a, b, c (Å) | 54.41, 54.41, 96.53 | 54.56, 54.56, 97.50 |
| α = β = γ (°) | 90 | 90 |
| Wavelength (Å) | 0.9774 | 0.9791 |
| Resolution (Å) | 47.4 (2.382–2.300) | 38.58 (2.54–2.51) |
| Rmerge | 11.2 (44.4) | 9.7 (34.5) |
| Average I/σI | 33.8 (7.0) | 22.1 (7.5) |
| Completeness (%) | 99.8 (99.1) | 98.0 (97.7) |
| Multiplicity | 22.9 (22.6) | 11.5 (11.7) |
| Total reflections | 157,974 (15,107) | 79,606 (7814) |
| Unique reflections | 6909 (662) | 5444 (603) |
| CC1/2 | 99.4 (98.2) | 98.9 (98.7) |
| Solvent content (%) | 41.2 | 42.1 |
| SAD phasing | ||
| Figure of merit | 0.33 | |
| Refinement | ||
| Rwork/Rfree | 20.77/24.90 | |
| RMS deviations | ||
| Bond lengths (Å) | 0.008 | |
| Bond angles (°) | 1.049 | |
| Number of atoms | ||
| All atoms | 1030 | |
| Protein | 962 | |
| Ligand | 44 | |
| Water | 24 | |
| Ramachandran statistics | ||
| Favorable (%) | 99.17 | |
| Additionally allowed (%) | 0.83 | |
| Outlier (%) | 0 | |
CDA, 3′, 5′-cyclic di-adenosine monophosphate (c-di-AMP); SAD, single-wavelength anomalous dispersion; USP, universal stress protein; USPSa, S. aureus KdpD-USP.
Rwork = Σ ∥Fo|−|Fc∥/Σ |Fo|, calculated with a working set of reflections. Rfree is Rwork calculated with only the test set with 10% of reflections. Data for the highest resolution shell are given in parentheses. The structures were determined using single crystals. The reflections I(+) and I(−), related by Friedel's Law, were treated as independent for the purpose of the SAD data only.