TABLE 5.
Crystallization conditions, data collection, and refinement statistics for VcIMPDHΔL complexes
ASU indicates asymmetric unit.
| VcIMPDHΔL·IMP·NAD+ | VcIMPDHΔL·XMP·NADH | |
|---|---|---|
| Data collection | ||
| Space group | P4212 | P4212 |
| Cell dimensions | ||
| a, b, c (Å) | 121.33, 121.33, 94.47 | 91.26, 91.26, 171.21 |
| α, β, γ (°) | 90.00, 90.00, 90.00 | 90.00, 90.00, 90.00 |
| Protein molecules/ASU | 2 | 2 |
| Wavelength (Å) | 0.9792 | 0.9792 |
| Resolution (Å)a | 2.32 (2.32-2.36) | 1.62 (1.65-1.62) |
| Unique reflections | 31196 (1529) | 92477 (4551) |
| Rmergeb | 0.104 (0.918) | 0.067 (0.743) |
| 〈I/σI〉 | 8.8 (2.1) | 10.8 (2.8) |
| Completeness (%) | 100 (100) | 100 (100) |
| Redundancy | 8.7 (6.6) | 8.2 (7.8) |
| Refinement | ||
| Resolution (Å) | 2.32 (2.32-2.38) | 1.62 (1.62-1.66) |
| Reflections: work/test set | 29325/1553 | 87862/4552 |
| Rwork/Rfreec | 0.200 (0.270) | 0.151 (0.181) |
| No. of atoms: protein/ligandsd/water | 5064/136/178 | 5208/165/563 |
| Average B factor (Å2): protein/ligands/water | 43.9/58.4/42.1 | 23.3/28.6/34.7 |
| Bond lengths (Å) | 0.016 | 0.015 |
| Bond angles (°) | 1.852 | 1.936 |
| Most favored | 96.8 | 97.6 |
| Outliers | 0.1 | 0.0 |
| PDB code | 4QNE | 4X3Z |
| Crystallization conditions | 0.77 m sodium/potassium phosphate, 0.15 m Tris-HCl, pH 8.0, 6% MPD, 16 °C | 1.03 m sodium/potassium phosphate, pH 5.0, 0.15 m sodium malate, 3% PEG 300, 16 °C |
| Soak with 200 mm NAD+ solution | 15 min, 20 °C | 5 days, 16 °C |
| Cryo-protection solution | 25% sucrose | 25% glycerol |
a Values in parentheses correspond to the highest resolution shell.
b Rmerge = ΣhklΣi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣi|〈Ii(hkl)〉 , where Ii(hkl) is the intensity for the ith measurement of an equivalent reflection with indices h, k, and l.
c R = Σhkl‖Fobs| − |Fcalc‖/Σhkl|Fobs|, where Fobs and Fcalc are observed and calculated structure factors, respectively. Rfree is calculated analogously for the test reflections, which were randomly selected and excluded from the refinement.
d Ligands include all atoms, excluding protein and water atoms.