TABLE 1.
Crystallographic data processing and refinement statistics for levoglucosan kinase crystallographic structures
| PDB ID (ligand) |
|||||
|---|---|---|---|---|---|
| 4ZFV (ADP/Mg) | 4YH5 (ADP/Mn) | 4ZLU (ADP/Mg/LG) | 5BVC (ADP/Mg/LG (alternate)) | 5BSB (LG) | |
| Data collectiona | |||||
| Space group | P41212 | P41212 | P41212 | P41212 | P41212 |
| Unit cell (Å) | a = b = 114.40, c = 232.50 | a = b = 114.44, c = 232.48 | a = b = 114.86, c = 234.77 | a = b = 70.25, c = 264.19 | a = b = 70.32, c = 263.33 |
| α = β = γ = 90.00 | α = β = γ = 90.00 | α = β = γ = 90.00 | α = β = γ = 90.00 | α = β = γ = 90.00 | |
| Wavelength (Å) | 0.9795 | 1.8920 | 0.9795 | 1.1271 | 0.9795 |
| Resolution range (Å) | 47.20–1.50 (1.58–1.50) | 47.21–1.90 (2.00–1.90) | 47.57–1.80 (1.90–1.80) | 43.27–2.00 (2.11–2.00) | 48.86–1.85 (1.95–1.85) |
| Total observations | 1,365,581 | 2,394,174 | 567,803 | 148,841 | 325,310 |
| Total unique observations | 244,767 | 121,746 | 145,247 | 44,939 | 57,761 |
| I/σI | 10.3 (2.1) | 21.6 (4.2) | 9.1 (2.2) | 6.2 (2.0) | 9.8 (1.9) |
| Completeness (%) | 99.9 (100.0) | 99.9 (99.1) | 99.9 (99.7) | 98.5 (99.9) | 100.0 (100.0) |
| Rmerge | 0.099 (0.787) | 0.104 (0.569) | 0.101 (0.719) | 0.100 (0.592) | 0.096 (0.861) |
| Rpim | 0.045 (0.363) | 0.024 (0.175) | 0.059 (0.397) | 0.062 (0.368) | 0.043 (0.395) |
| Redundancy | 5.6 (5.5) | 19.7 (11.2) | 3.9 (4.2) | 3.3 (3.4) | 5.6 (5.7) |
| Anomalous completeness (%) | 99.8 (98.5) | ||||
| Anomalous multiplicity | 10.2 (5.6) | ||||
| Refinement statistics | |||||
| Resolution (Å) | 47.20–1.50 | 47.21–1.90 | 47.10–1.80 | 43.3–2.00 | 48.86–1.85 |
| Reflections (total) | 244,650 | 121,618 | 145,033 | 44,796 | 57,602 |
| Reflections (test) | 12,339 | 6081 | 7286 | 2271 | 2897 |
| Total atoms refined | 8309 | 7824 | 7762 | 3610 | 3680 |
| Solvent | 1440 | 1032 | 1001 | 292 | 359 |
| Rwork (Rfree) | 0.16 (0.17) | 0.16 (0.17) | 0.19 (0.22) | 0.20 (0.23) | 0.19 (0.22) |
| RMSDsb (bond lengths (Å)/angles (°)) | 0.007/1.095 | 0.007/1.069 | 0.008/1.145 | 0.008/1.117 | 0.006/1.035 |
| Ramachandran plot (favored/allowed (%)) | 98.1/1.7 | 98.3/1.5 | 98.3/1.5 | 97.7/2.1 | 97.2/2.6 |
| Mean B values (Å2) | |||||
| Overall protein chain (A/B) | 15.7/17.0 | 20.1/21.6 | 20.4/27.2 | 28.0 | 29.6 |
| ADP | 13.0/15.5 | 18.3/20.6 | 21.5/74.9 | 50.6 | |
| Mg or Mn | 12.6,12.4/13.6,13.7 | 27.3,28.3/29.2,29.5 | 23.8, 20.8 | 42.0 | |
| LG | 30.3/25.5 | 20.8 | 26.4 | ||
| Active site Tris | 26.9 | ||||
a Values in parentheses refer to the high-resolution shell.
b RMSDs, root mean square deviations.