Table 3.
X-ray data collection and structure refinement statistics for S. Montevideo DpdA
| Data collection | |||
|---|---|---|---|
| Space group | P21212 | ||
| Matthew's coefficient (Å3/Da) | 2.77 | ||
| Solvent content (%) | 55.6 | ||
| Monomers/AU | 1 | ||
| Dataset | Peak | Remote | Inflection |
| Unit cell a, b, c (Å) | 86.10, 141.77, 42.50 | 86.12, 141.83, 42.50 | 86.13, 141.88, 42.51 |
| Wavelength (Å) | 1.28149 | 0.98397 | 1.28268 |
| Resolution (Å)a | 73.59–2.51 (2.65–2.51) | 73.61–2.65 (2.79–2.65) | 73.62–2.59 (2.73–2.59) |
| Measured reflections | 207 845 (11 600) | 225 828 (32 623) | 201 380 (13 261) |
| Unique reflections | 16 179 (1324) | 15 829 (2245) | 15 462 (1439) |
| Completeness (%) | 87.1 (50.4) | 100 (100) | 90.8 (59.6) |
| Multiplicity | 12.8 (8.8) | 14.3 (14.5) | 13.0 (9.2) |
| R-merge (%) | 0.103 (0.964) | 0.197 (1.488) | 0.105 (0.873) |
| R-meas (%) | 0.107 (1.025) | 0.204 (1.542) | 0.109 (0.925) |
| R-pim (%) | 0.029 (0.341) | 0.054 (0.400) | 0.040 (0.412) |
| CC1/2 | 0.99 (0.92) | 1.0 (0.88) | 1.0 (0.93) |
| <I/σ(I)> | 21.8 (2.3) | 15.1 (2.5) | 22.4 (2.8) |
| FOM after density modification 0.68 | |||
| No. of Zn sites 1 | |||
| Structure refinement | |||
| Resolution range (Å) | 54.78–2.51 (2.57–2.51) | ||
| No. of reflections | 15 348 (571) | ||
| No. of atoms in the asymmetric unit | |||
| Protein/water/Zn2+ | 3368/91/1 | ||
| Rcryst/Rfreeb | 0.132/0.179 | ||
| Deviation from ideality | |||
| Bond length (Å) | 0.006 | ||
| Bond angles (°) | 1.078 | ||
| Ramachandran plot—residues in: | |||
| Favored (%) | 96.6 | ||
| Allowed (%) | 2.9 | ||
| Outliers (%)c | 0.5 | ||
| Mean B factor (Å2) | 55.9 | ||
| Estimated coordinate error (Å)d | 0.23 | ||
aHighest resolution shell information in parentheses; bRfree was monitored with 5% of the data excluded from the refinement; ctwo outliers, Gln33 and Arg384, both ordered residues and engaged in hydrophilic interactions with their envirnments; dvalue calculated based on Rfree.