Table 2.
Crystallographic data.
| Dataset | Aureolysin/wt-IMPI | Aureolysin/I57F-IMPI (1) | Aureolysin/I57F-IMPI (2) |
|---|---|---|---|
| Beam line (synchrotron) | XALOC (ALBA) | ID23-2 (ESRF) | XALOC (ALBA) |
| Space group/complexes per a.u. a | P41/2 | P41212/1 | P41/2 |
| Twinning fraction α (−k,−h,−l) | 0.49 | 0.380 (estimated for P41) | 0.536 |
| Cell constants (a and c in Å) | 68.14, 166.18 | 68.80, 167.25 | 68.08, 166.69 |
| Wavelength (Å) | 0.97926 | 0.87313 | 0.97926 |
| Measurements/unique reflections | 874,126/64,323 | 326,552/26,086 | 398,888/99,152 |
| Resolution range (Å) (outermost shell) c | 52.7–1.85 (1.96–1.85) | 68.8–2.05 (2.17–2.05) | 68.1–1.60 (1.70–1.60) |
| Completeness (%)/Rmerged | 100.0 (99.8)/0.149 (2.772) | 100.0 (99.9)/0.193 (1.808) | 99.7 (99.4)/0.050 (1.069) |
| Rpime/CC(1/2) e | 0.042 (0.788)/0.999 (0.630) | 0.069 (0.712)/0.997 (0.641) | 0.029 (0.618)/0.999 (0.580) |
| Average intensity f | 14.7 (1.9) | 9.4 (1.6) | 14.2 (1.8) |
| B-Factor (Wilson) (Å2)/Aver. multiplicity | 42.2/13.6 (13.4) | 41.9/12.5 (13.4) | 34.4/4.0 (4.0) |
| Resolution range used for refinement (Å) | 52.7–1.85 | 68.1–1.60 | |
| Reflections used (test set) | 63,598 (724) | 98,470 (681) | |
| Crystallographic Rfactor (free Rfactor) d | 0.164 (0.219) | 0.158 (0.188) | |
| Non-H protein atoms/ionic ligands/ | 6467/6 Ca2+, 2 Zn2+ | 6322/6 Ca2+, 2 Zn2+ | |
| waters/non-ionic ligands per a.u. | 709/2 PEG, 3 EDO | 559/5 EDO | |
| Rmsd from target values | |||
| bonds (Å)/angles (°) | 0.008/1.64 | 0.008/1.76 | |
| Average B-factor (Å2) | 38.1 | 32.6 | |
| Protein contacts and geometry analysis b | |||
| Ramachandran favoured/outliers/all analysed | 686 (95.0%)/0/722 | 691 (95.5%)/1/723 | |
| Bond-length/bond-angle/chirality/planarity outliers | 0/3/0/2 | 0/2/0/3 | |
| Side-chain outliers | 22 (3.6%) | 15 (2.5%) | |
| All-atom clashes/clashscore b | 15/1.3 | 20/1.7 | |
| RSRZ outliers b/Fo:Fc correlation | 2 (0.3%)/0.97 (0.95) | 7 (1.0%)/0.98 (0.97) | |
| PDB access code | 7SKM | 7SKL |
a
Abbreviations: EDO, ethylene glycol; PEG, diethylene glycol; RSRZ, real-space R-value Z-score.
b
According to the wwPDB Validation Service (https://wwpdb-validation.wwpdb.org/validservice).
c
Values in parenthesis refer to the outermost resolution shell if not otherwise indicated.
f
Average intensity is 〈I/σ(I)〉 of unique reflections after merging according to XSCALE[70].