TABLE 1.
Statistics of x-ray data collection and structure refinement
Values in parentheses refer to the highest resolution shell. SAD, single anomalous dispersion; r.m.s., root means square; CC, correlation coefficient; ESRF, European Synchrotron Radiation Facility; SLS, Swiss Light Source.
| Parameter | Native data set (Protein Data Bank code 4Y7T) | NH4I-soaked for SAD phasing | MurNAc-α1-P + UppNHp, complex 1 (Protein Data Bank code 4Y7V) | Mg2+ + MurNAc-α1-P + UpNHpp, complex 2 (Protein Data Bank code 4Y7U) |
|---|---|---|---|---|
| Data collection | ||||
| Beamline | ID14-4, ESRF | X06DA, SLS PXIII | X06DA, SLS PXIII | X06DA, SLS PXIII |
| Wavelength (Å) | 1.0 | 1.7 | 1.0 | 1.0 |
| Space group | P 6122 | P 6122 | P 6122 | P 6122 |
| Cell dimensions | ||||
| a, b, c (Å) | 72.61, 72.61, 158.47 | 72.71, 72.71, 159.01 | 72.35, 72.35, 162.48 | 72.75, 72.75, 163.13 |
| α, β, γ (°) | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 | 90.0, 90.0, 120.0 |
| Resolution (Å) | 50.0-1.8 (1.9-1.8) | 30.0-2.4 (2.4-2.4) | 50.0-1.8 (2.1-1.8) | 50.0-1.7 (2.0-1.7) |
| |I/σ| | 13.3 (2.0) | 44.8 (9.8) | 27.1 (2.0) | 30.7 (2.1) |
| |I/σ| of anomalous signal | 1.8 (0.84) | |||
| CC1/2 (%) | 99.9 (88.9) | 100.0 (98.4) | 100.0 (80.6) | 100.0 (84.2) |
| Rmeas (%) | 22.4 (804.6) | 7.9 (52.3) | 9.3 (236.9) | 6.4 (200.2) |
| Rpim (%) | 4.1 (193.3) | 1.2 (8.3) | 1.5 (38.0) | 1.0 (33.3) |
| Completeness (%) | 99.9 (99.6) | 99.9 (100.0) | 99.9 (100.0) | 100.0 (100.0) |
| Measured reflections | 704,884 | 741,478 | 916,020 | 1,044,585 |
| Unique reflections | 23,701 | 18,399 | 24,133 | 28,942 |
| Redundancy | 29.7 | 40,3 | 38.0 | 36.1 |
| Wilson B (Å2) | 44.2 | 43,6 | 47.1 | 46.7 |
| Refinement | ||||
| Resolution (Å) | 40.4-1.8 | 49.6-1.8 | 49.8-1.7 | |
| Rwork/Rfree (%) | 21.1/24.5 | 21.5/25.4 | 22.8/26.4 | |
| No. of atoms | ||||
| Protein | 1,683 | 1,652 | 1,702 | |
| H2O | 80 | 67 | 54 | |
| Ligands: | ||||
| MurNAc/-1-P | 41 | 24a | ||
| UxxP/UDP | 14 | 29a | ||
| SO42− | 20 | 5 | 5 | |
| Mg2+/Na+/NH4+ | 2 | |||
| Glycerol | 42 | 28 | 28 | |
| Total | 1,783 | 1,807 | 1,791 | |
| B-factors (Å2) | ||||
| Protein | 46.68 | 51.84 | 55.95 | |
| H2O | 49.96 | 56.86 | 53.13 | |
| Ligands | ||||
| MurNAc/-1-P | 48.71 | 68.05 | ||
| UxxP/UDP | 86.05 | 106.52 | ||
| Mg2+/Na+/NH4+ | 6.95 | |||
| SO42− | 88.38 | 94.51 | 105.33 | |
| Glycerol | 48.38 | 57.29 | 71.61 | |
| r.m.s.a deviations | ||||
| Bond length (Å) | 0.015 | 0.007 | 0.008 | |
| Bond angles (°) | 1.526 | 1.074 | 1.192 | |
| Ramachandran plot | ||||
| Favored regions (%) | 94.17 | 98.17 | 93.04 | |
| Allowed regions (%) | 4.93 | 1.83 | 6.09 | |
| Outliers (%) | 0.90 | 0.00 | 0.87 | |
a Ligands refined without hydrogens.