TABLE 1.
Data collection, phasing, and refinement statistics
|
FomA·DPO
|
FomA·MgAMPPNP· fosfomycin
|
SeMet FomA·DPO
|
|||
|---|---|---|---|---|---|
| λ1 (peak) | λ2 (inflection) | λ3 (remote) | |||
| Wavelength (Å) | 1.38079 | 1.38074 | 0.9793 | 0.9795 | 0.9537 |
| Resolution (Å) | 1.53 | 2.20 | 1.45 | 1.45 | 1.45 |
| Temperature (K) | 113 | 113 | 113 | 113 | 113 |
| Space group | P3221 | P3221 | P3221 | ||
| Cell dimensions | |||||
| a (Å) | 88.36 | 85.66 | 88.30 | ||
| c (Å) | 79.05 | 78.98 | 78.87 | ||
| Number of molecules/asymmetric unit | 1 | 1 | 1 | ||
| No. of unique reflections | 52 986 | 17 293 | 55 525 | 61 104 | 55 632 |
| Rsym (%)a,b | 4.0 (51.0) | 7.1 (55.7) | 6.2 (64.2) | 5.7 (53.6) | 6.8 (70.0) |
| Completeness (%) | 97.9 (85.3) | 99.6 (97.9) | 97.1 (100.0) | 96.6 (100.0) | 87.4 (90.8) |
| Redundancies | 5.2 (4.6) | 4.1 (3.4) | 7.3 (7.5) | 9.2 (9.4) | 12.8 (11.8) |
| I/σ(I) | 34.8 (2.9) | 19.2 (1.8) | 22.6 (3.0) | 32.0 (4.0) | 28.0 (3.4) |
| Phasing statistics | |||||
| Resolution range (Å) | 30–1.6 | ||||
| Number of sites | 5 | ||||
| Phasing power acentric/centricc | 2.68/2.91 | ||||
| Rc centricd | 0.39 | ||||
| Mean FOM after multiple wavelength anomalous dispersion phasing | 0.666 | ||||
| Refinement statistics | |||||
| Resolution range (Å) | 27.49–1.53 | 29.04–2.20 | |||
| No. of reflections used in refinement | 50 201 | 15 587 | |||
| σ cut-off used in refinement | none | none | |||
| R/Rfree (%)e | 16.86/19.80 | 19.26/25.20 | |||
| Number of refined atoms | |||||
| Protein | 1953 | 2034 | |||
| Heterogen atoms | 9 | 40 | |||
| Water | 231 | 60 | |||
| Average B-factors (Å2) | |||||
| Protein | 25.8 | 43.2 | |||
| Water | 35.8 | 42.7 | |||
| DPO | 41.9 | ||||
| AMPPNP | 44.1 | ||||
| Magnesium | 44.7 | ||||
| Root mean square deviations | |||||
| Bonds (Å) | 0.016 | 0.014 | |||
| Angles (°) | 1.738 | 1.727 | |||
| Ramachandran plot (%) | |||||
| Favored | 93.3 | 90.7 | |||
| Allowed | 6.7 | 8.8 | |||
| Generous | 0 | 0.4 | |||
| Disallowed | 0 | 0 | |||
The values in parentheses are for the highest resolution shell
Rsym = Σ|Ii – <Ii>|/ΣIi, where Ii is the intensity of the ith observation and <Ii> is the mean intensity of the reflection
Phasing power = Σ<Fh>/E, where <Fh> is the root mean square structure factor, and E is the residual lack of closure error
Rc = Σ||FpH ± Fp| – FHcalc|/Σ FpH ± Fp, where FpH and Fp are the structure factor amplitudes for the data collection on the selenium absorption edge
R = Σ||Fo| – |Fc||/Σ|Fo|, where Fo and Fc are the observed and calculated structure factors amplitudes. Rfree is calculated using 1.6 and 1.4% of reflections omitted from the refinement for the FomA·DPO and FomA·MgAMPPNP·fosfomycin structures, respectively