TABLE 1.
Data collection and refinement statistics
| Parameter | LmPBPD2 (apo) |
LmPBPD2 (acylated) in complex with: |
|||
|---|---|---|---|---|---|
| Penicillin G | Ampicillin | Cefotaxime | Cefuroxime | ||
| Data collection | |||||
| Space group | P212121 | P21 | P21 | P21 | P21 |
| Cell dimensions | |||||
| a, b, c (Å) | 37.7, 74.6, 75.0 | 74.7, 98.9, 77.5 | 74.9, 98.9, 77.4 | 74.9, 98.7, 154.6 | 75.0, 99.3, 155.1 |
| α, β, γ (°) | 90, 90, 90 | 90, 104.3, 90 | 90, 104.2, 90 | 90, 103.9, 90 | 90, 103.9, 90 |
| Resolution (Å) | 40–1.6 | 30–1.9 | 30–1.7 | 30–1.9 | 30–2.0 |
| Rsymb (%) | 8.8 (33.1)a | 14.6 (47.2) | 10.3 (29.3) | 14.6 (43.9) | 12.7 (47.5) |
| I/σ (I) | 34.3 (4.3) | 19.8 (4.6) | 17.7 (2.2) | 6.6 (1.8) | 11.7 (2.7) |
| Completeness (%) | 98.2 (79) | 98.4 (97.4) | 92.8 (85.2) | 97.4 (96.4) | 99.8 (99.7) |
| Redundancy | 5.8 (3.4) | 6.5 (6.5) | 3.9 (2.5) | 3.3 (3.4) | 6.1 (5.9) |
| Structure refinement | |||||
| Resolution (Å) | 37.3–1.6 | 30.0–1.9 | 30.0–1.7 | 30–2.0 | 30.0–2.0 |
| No. of reflections | 30,732 | 84,570 | 110,752 | 170,471 | 136,600 |
| Rwork/Rfreec | 16.5/18.9 | 21.6/24.9 | 22.9/25.9 | 21.7/24.0 | 20.0/23.5 |
| RMSD (bond lengths [Å]/angles [°]) | 0.006/1.01 | 0.007/0.88 | 0.006/0.86 | 0.007/0.83 | 0.007/0.85 |
| Average B-factor (Å2) | 14.8 | 21.6 | 23.6 | 19.2 | 16.1 |
| MolProbity statistics | |||||
| Ramachandran favored/outlier (%) | 98.8/0 | 98.4/0 | 98.1/0 | 97.13/0 | 97.4/0 |
| Rotamer outlier (%) | 0 | 1.47 | 0.97 | 0.06 | 0 |
| Clashscored | 1.32 | 8.29 | 3.75 | 2.93 | 5.23 |
| Overall scored | 0.86 | 1.58 | 1.16 | 1.24 | 1.41 |
a
The numbers in parentheses are statistics from the highest-resolution shell.
b
Rsym = Σ |Iobs − Iavg|/Iobs, where Iobs is the observed intensity of individual reflection and Iavg is the average over symmetry equivalents.
c
Rwork = Σ ||Fo| − |Fc||/Σ |Fo|, where |Fo| and |Fc| are the observed and calculated structure factor amplitudes, respectively. Rfree was calculated with 5% of the data.
d
Scores are ranked according to structures of similar resolution as formulated in MolProbity software.