TABLE 3.
Crystallographic data collection and model refinement statistics for the structures of S. cerevisiae HADs: RHR2, UTR4, and YKR070W
| RHR2 | SDT1 | YKR070W | YKR070W·Gly-3-P | |
|---|---|---|---|---|
| Data collection | ||||
| PDB code | 2QLT | 3NUQ | 3KC2 | 3RF6 |
| Space group | P212121 | P21212 | C2 | P212121 |
| Unit cell (Å) | a = 40, b = 56, c = 98 | a = 58, b = 65, c = 68 | a = 144, b = 67, c = 77, β = 110º | a = 60, b = 72, c = 195 |
| Wavelength (Å) | 0.9794 | 1.54 | 0.9794 | 0.9794 |
| Resolution (Å) | 22.9–1.60 | 23.4–1.60 | 40–1.55 | 35.2–1.70 |
| No. of unique reflections | 29,314 | 32,965 | 99,266 | 93,836 |
| Average redundancy | 14.4 | 5.7 | 3.55 | 6.0 |
| Rmergea (%) | 0.094 (0.51) | 0.077 (0.35) | 0.063 (0.74) | 0.066 (0.93) |
| Completeness (%) | 99.9 (100) | 95.5 (65.3) | 99.6 (98.9) | 99.8 (100) |
| I/C | 47.7 (4.43) | 14.9 (2.40) | 24.3 (1.90) | 30 (1.80) |
| Refinement statistics | ||||
| Rcryst (%) | 16.8 | 19.4 | 14.5 | 16.4 |
| Rfree (%) | 19.5 | 22.6 | 16.9 | 19.4 |
| Protein residues/solvent | 250/248 | 280/136 | 679/880 | 691/545 |
| Ligands | 1Ca2+/1Cl − /4Hg2+/4SO42 − /2EDO | 1Na+/2 Cl−/1PEG/ 2EDO | 3 Mg2+/4PO42 − | 3Mg2+/2G3P/ 2FLC |
| r.m.s. deviation from target values | ||||
| Bond lengths (Å) | 0.014 | 0.012 | 0.016 | 0.021 |
| Bond angles (degrees) | 1.55 | 1.40 | 1.51 | 1.53 |
| Average B factors (Å2) | ||||
| Protein whole chains | 19.7 | 17.23 | 10.81 | 33.16 |
| Solvent | 29.0 | 34.30 | 22.40 | 36.13 |
| Ligands | 15.4/23.5/23.5/29.0/ 30.1/35.3 | 13.6/58.3/58.9/ 19.5 | 13.8/23.5 | 27.7/34.1/50.5 |
| Ramachandran plotb (%) | 91.7/8.3/—c | 93.4/6.6/— | 92.7/7.3/— | 92.3/7.7/— |
a Numbers in parentheses are values for the highest resolution bin.
b Ramachandran plot statistics; favored/allowed/outlier.
c —, no outlier.