Table 2.
Crystallographic Data Collection and Model Refinement Statisticsa
| YbaSb tetragonal | YbaS (1u60) | YbgJb (1mki) | YbgJ + DON (3brm) | |
|---|---|---|---|---|
| Data Collection | ||||
| space group | I4 | P212121 | P21212 | P21212 |
| cell dimensions | ||||
| a(Å) | 239.8 | 50.5 | 71.3 | 71.2 |
| b(Å) | 155.9 | 81.5 | 184.7 | |
| c(Å) | 50.1 | 164.2 | 51.5 | 51.4 |
| wavelength | 0.97948 | 0.97978 | 0.9793 | 0.9793 |
| resolution (Å) | 50–1.8 (1.86–1.8) | 50–1.8 (1.86–1.8) | 50–2.0 (2.07–2.0) | 50–2.29 (2.38–2.29) |
| Rsym or Rmerge | 0.079 (0.388) | 0.046 (0.153) | 0.109 (0.502) | 0.138 (0.521) |
| I/σI | 27.7 (2.2) | 25.6 (5.4) | 5.4 (3.7) | 5.2 (1.9) |
| completeness (%) | 97.9 (83.4) | 93.2 (75.2) | 99.1 (98.5) | 97.6 (83.8) |
| redundancy | 6.8 (2.8) | 3.9 (3.0) | 10.2 (9.6) | 6.3 (4.0) |
| Refinement | ||||
| resolution (Å) | 40–1.80 | 40.7–2.0 | 34.5–2.29 | |
| no. of reflections | 107720/5686 | 43940/4346 | 24770/1317 | |
| Rwork/Rfree | 0.143/0.178 | 0.212/0.245 | 0.174/0.248 | |
| no. of atoms | ||||
| protein | 9258 | 4844 | 4500 | |
| major ligand | 75 | 16 | 20 | |
| solvent | 1150 | 333 | 295 | |
| average B-factors | ||||
| overall | 19.2 | 31.3 | 32.9 | |
| protein | 17.2 | 30.9 | 32.3 | |
| waters | 33.8 | 36.4 | 42.2 | |
| ligand/otherc | 39.9 | 42.6 | 42.4 | |
| Wilson B-factor | 17.1 | 15.2 | 32.4 | |
| rms deviations | ||||
| bond lengths (Å) | 0.015 | 0.006 | 0.018 | |
| bond angles (deg) | 1.4 | 1.3 | 1.7 | |
| Ramachandran plot | ||||
| % in most favored regions | 90.8 | 89.6 | 92.6 | |
| % in additionally allowed regions | 8.0 | 8.9 | 6.5 | |
| % in disallowed regions | 0.4 | 0.6 | 0.0 | |
a
Values in parentheses are for the highest resolution shell.
b
Data collection statistics are reported for data collection at the selenium peak wavelength; data were also collected for the inflection and remote wavelengths, but these are reported in the Supporting Information table.
c
In the YbgJ + DON covalent complex, this refers to the average temperature factors for the ligand 5-oxo-l-norleucine. In the other glutaminase structures, there was no ligand, but molecules of 1,2-ethylene glycol and formate ions were found.