Table 1. Crystallographic data.
| Promirolysin (SeMet)† | Promirolysin (SeMet) | Promirolysin (native) | Mirolysin (product complex) | |
|---|---|---|---|---|
| Data processing | ||||
| Space group, protein molecules per asymmetric unit | P21, 2 | P21, 2 | P212121, 1 | P212121, 1 |
| Cell constants (a, b and c in Å, β in °) | 47.78, 79.21, 75.50, 106.80 | 47.78, 79.21, 75.50, 106.80 | 47.33, 67.25, 79.64, 90.0 | 40.61, 66.49, 96.22, 90.0 |
| Wavelength (Å) | 1.2815 | 1.2815 | 1.2816 | 0.9792 |
| No. of measurements/unique reflections | 341819/134930 | 340267/70233 | 487729/50157 | 517385/41508 |
| Resolution range (Å)‡ | 53.4–1.60 (1.70–1.60) | 53.4–1.60 (1.70–1.60) | 51.4–1.40 (1.48–1.40) | 54.7–1.50 (1.59–1.50) |
| Completeness (%) | 96.4 (96.0) | 98.9 (99.1) | 98.7 (92.0) | 97.6 (90.4) |
| R merge | 0.097 (0.857) | 0.114 (0.983) | 0.076 (1.041) | 0.038 (0.235) |
| R meas/CC1/2 | 0.121 (1.068)/0.993 (0.635) | 0.128 (1.104)/0.996 (0.709) | 0.080 (1.119)/0.999 (0.719) | 0.040 (0.245)/1.000 (0.989) |
| 〈I/σ(I)〉 of unique reflections after merging | 8.8 (1.7) | 10.9 (2.4) | 13.8 (1.8) | 41.3 (14.8) |
| B factor (Wilson) (Å2)/average multiplicity | 25.4/2.5 (2.4) | 25.0/4.8 (4.7) | 25.6/9.7 (7.1) | 25.6/12.5 (11.7) |
| Structure refinement | ||||
| No. of reflections used in refinement (in test set) | 69544 (688) | 49412 (722) | 40780 (728) | |
| Crystallographic R factor/free R factor | 0.186/0.220 | 0.161/0.188 | 0.144/0.158 | |
| Correlation coefficient F obs − F calc (test set)§ | 0.942 (0.915) | 0.971 (0.960) | 0.965 (0.967) | |
| No. of protein residues/atoms/solvent molecules/non-covalent ligands | 616/4856/445/2 Zn2+, 4 Ca2+, 4 glycerol, 1 boric acid | 307/2430/274/1 Zn2+, 2 Ca2+, 4 glycerol | 284/2239/348/1 Zn2+, 2 Ca2+, 2 ethanol, 1 citrate | |
| R.m.s.d. from target values bonds (Å)/angles (°) | 0.012/1.14 | 0.010/1.01 | 0.010/1.02 | |
| Average B factors (Å2) (overall/molecule A/molecule B) | 21.7/20.0/22.1 | 25.4/24.3/— | 17.9/15.2/32.2 | |
| All-atom contacts and geometry analysis¶ | ||||
| Protein residues in favoured regions/outliers/all residues | 602 (96.6%)/4††/623‡‡ | 304 (96.2%)/3††/316‡‡ | 284 (96.9%)/1††/293‡‡ | |
| Outlying rotamers/bonds/angles/chirality/planarity | 12 (2.2%)/0/1/0/0 | 4 (1.4%)/0/0/0/0 | 3 (1.2%)/0/0/0/0 | |
| All-atom clashscore | 2.8 | 1.9 | 0.4 | |
| PDB access code | 6r7u | 6r7v | 6r7w |
†
For phasing, Friedel pairs were kept separately.
‡
Data processing values in parentheses are for the outermost resolution shell.
§
According to the final BUSTER/TNT refinement step.
¶
According to the wwPDB X-ray structure validation report.
††
All outliers were unambiguously resolved in the final Fourier maps.
‡‡
Including residues with atoms in two positions.