Table 2.
X-ray data collection statistics and model refinement statistics
| X-ray data and model parameters | Pcryo_0638 | Pcryo_0637 UDP/acetyl-CoA | Pcryo_0637 CoA/UDP-2,4-diacetamido-2,4,6-trideoxy-d-glucose | Pcryo_0637 CoA/UDP-2-acetamido-4-amino-2,4,6-trideoxy-d-glucose | Pcryo_0637 tetrahedral intermediate |
|---|---|---|---|---|---|
| Resolution limits (Å) | 50.0–1.30 (1.40–1.30)a | 50.0–1.30 (1.40–1.30)a | 50.0–1.55 (1.65–1.55)a | 50.0–1.30 (1.40–1.30)a | 50.0–1.40 (1.50–1.40)a |
| Number of independent reflections | 202026 (36,011) | 56,307 (11,060) | 33,312 (5566) | 56,136 (10,804) | 45,470 (8481) |
| Completeness (%) | 92.9 (83.0) | 98.2 (96.6) | 98.1 (95.0) | 98.3 (94.6) | 98.8 (97.9) |
| Redundancy | 2.4 (1.9) | 6.1 (2.8) | 5.1 (2.4) | 8.1 (2.5) | 5.9 (3.3) |
| avg I/avg σ(I) | 7.2 (1.9) | 17.6 (3.0) | 19.6 (3.0) | 20.3 (2.4) | 20.2 (3.3) |
| Rsym (%)b | 5.7 (22.9) | 6.2 (43.6) | 4.5 (34.1) | 5.4 (44.8) | 4.9 (38.0) |
| cR-factor (overall)%/no. reflections | 15.1/202026 | 19.5/56,307 | 16.4/33,312 | 17.7/56,136 | 15.9/45,470 |
| R-factor (working)%/no. reflections | 15.0/191942 | 19.4/53,390 | 16.2/31,600 | 17.3/53,279 | 15.8/43,279 |
| R-factor (free)%/no. reflections | 16.9/10,084 | 21.4/2917 | 19.0/1712 | 19.4/2857 | 18.2/2191 |
| Number of protein atoms | 6354 | 1642 | 1635 | 1649 | 1651 |
| Number of heteroatoms | 1480 | 364 | 355 | 373 | 379 |
| Average B values | |||||
| Protein atoms (Å2) | 12.2 | 11.8 | 17.8 | 14.7 | 14.5 |
| Ligand (Å2) | 10.2 | 18.6 | 34.1 | 24.6 | 23.4 |
| Solvent (Å2) | 28.1 | 26.6 | 33.5 | 29.5 | 30.1 |
| Weighted RMS deviations from ideality | |||||
| Bond lengths (Å) | 0.010 | 0.010 | 0.009 | 0.010 | 0.010 |
| Bond angles (°) | 1.55 | 1.90 | 1.60 | 1.60 | 1.70 |
| Planar groups (Å) | 0.009 | 0.008 | 0.008 | 0.008 | 0.009 |
| Ramachandran regions (%)d | |||||
| Most favored | 98.6 | 94.9 | 95.8 | 96.3 | 95.8 |
| Additionally allowed | 1.4 | 5.1 | 4.2 | 3.7 | 4.2 |
| Generously allowed | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| PDB code | 7L7X | 7L7Y | 7L7Z | 7L81 | 7L82 |
Statistics for the highest resolution bin.
.
R-factor = (Σ|Fo - Fc|/Σ|Fo|) x 100 where Fo is the observed structure-factor amplitude and Fc is the calculated structure-factor amplitude.
Distribution of Ramachandran angles according to PROCHECK (26).