Table 1.
X-ray data collection and refinement statistics
| Crystal | SpoIIEPD 590–827 (aldohexose) | SpoIIEPD 590–827 (Mn) | SpoIIEPD 590–827 (SeMet peak) | SpoIIEPD 590–827 (SeMet inflection) | SpoIIEPD 590–827 (SeMet remote) |
|---|---|---|---|---|---|
| Data collection | |||||
| X-ray source | ID14-2, ESRF | ID14-4, ESRF | I02, DLS | I02, DLS | I02, DLS |
| Wavelength (Å) | 0.93300 | 0.93930 | 0.97950 | 0.97970 | 0.9755 |
| Resolution range (Å) | 50.00–2.6 | 50.00–2.76 | 50.00–3.5 | 50.00–3.5 | 50.00–3.5 |
| Space group | P6122 | P6122 | P6122 | P6122 | P6122 |
| Unit cell parameters | |||||
| a = b, c (Å) | 87.6, 321.6 | 86.0, 322.5 | 86.6, 316.9 | 86.6, 317.0 | 86.6, 317.0 |
| α = β, γ (°) | 90, 120 | 90, 120 | 90, 120 | 90, 120 | 90, 120 |
| Number of unique reflections, overall/outer shella | 23,618/1129 | 19,173/871 | 9693/459 | 9,64/460 | 9680/460 |
| Completeness (%), overall/outer shella | 99.9/98.3 | 99.5/94.8 | 100.0/100.0 | 99.8/100.0 | 99.8/100.0 |
| Redundancy, overall/outer shella | 7.3/4.3 | 16.8/16.1 | 39.5/40.3.2 | 19.9/20.5 | 19.9/20.6 |
| I/σ(I), overall/outer shella | 30.4/1.2 | 64.2/7.7 | 37.0.9/8.5 | 35.5/6.7 | 37.3/6.1 |
| Rmergeb (%), overall/outer shella | 6.5/89.0 | 6.6/39.4 | 14.9/52.6 | 12.7/47.0 | 12.6/48.1 |
| Refinement and model statistics | |||||
| Resolution range (Å) | 43.81–2.6 | 43.58–2.76 | |||
| R-factorc (Rfreed) | 0.23 (0.29) | 0.22 (0.30) | |||
| Reflections (working/free) | 22,278/1264 | 18,015/979 | |||
| Outer-shelleR-factorc (Rfreed) | 0.39 (0.38) | 0.27 (0.44) | |||
| Outer-shell reflections (working/free) | 1590/72 | 1273/73 | |||
| Molecules per asymmetric unit | 2 | 2 | |||
| Number of protein non-hydrogen atoms | 3393 | 3425 | |||
| Number of water and small-molecule atoms | 161 | 37 | |||
| rmsd from targetf | |||||
| Bond lengths (Å) | 0.008 | 0.020 | |||
| Bond angles (°) | 1.335 | 2.001 | |||
| Average B-factor (Å2) | 41.2 | 67.8 | |||
| Ramachandran plotg | 90.2/9.0/0.8/0.0 | 79.6/17.6/1.5/1.3 | |||
The outer shell corresponds to 2.64–2.60 Å [SpoIIEPD 590–827 (aldohexose)], 2.81–2.76 Å [SpoIIEPD 590–827 (Mn)] and 3.56–3.5 Å [SpoIIEPD 590–827 (SeMet)].
Rmerge = ∑hkl∑i|Ii − 〈I〉|/∑hkl∑i〈I〉, where Ii is the intensity of the ith measurement of a reflection with indexes hkl, and 〈I〉 is the statistically weighted average reflection intensity.
R-factor = ∑||Fo| − |Fc||/∑|Fo|, where Fo and Fc are the observed and calculated structure factor amplitudes, respectively.
Rfree is the R-factor calculated with 5% of the reflections chosen at random and omitted from refinement.
Outer shell for refinement corresponds to 2.600–2.663 Å (aldohexose), 2.833–2.762.
rmsd of bond lengths and bond angles from ideal geometry.
Percentage of residues in most favored/additionally allowed/generously allowed/disallowed regions of the Ramachandran plot.