Table 2.
Crystallography X-ray diffraction data collection and refinement statistics table
| Parameters and Statistics | Monoclinic Unliganded MsuD |
Monoclinic Binary-MsuD titrated soak |
Monoclinic Binary-MsuD soak |
Monoclinic Ternary-MsuD soak |
Hexagonal Ternary-MsuD cocrystal |
|---|---|---|---|---|---|
| Data Processing | |||||
| APS Beamline | 24-ID-E | 24-ID-E | 24-ID-C | 24-ID-C | 24-ID-C |
| Wavelength (Å) | 0.9792 | 0.9792 | 0.9795 | 0.9795 | 0.9795 |
| Resolution range (Å) | 64.79–2.80 (2.87–2.80)a | 65.03–2.80 (2.87–2.80) | 83.16–2.76 (2.83–2.76) | 82.21–2.75 (2.82–2.75) | 46.24–2.39 (2.450–2.39) |
| Space group | P 1 21 1 | P 1 21 1 | P 1 21 1 | P 1 21 1 | P 61 |
| a, b, c (Å) | 94.65 210.05 94.76 | 94.01 212.01 94.46 | 94.2 214.38 95.2 | 94.00 211.93 94.35 | 92.47 92.47 320.54 |
| α, β, γ (°) | 90 119.57 90 | 90 118.85 90 | 90 119.13 90 | 90 119.05 90 | 90 90 120 |
| Total reflections | 353,328 (26,137) | 483,126 (40,854) | 515,608 (52,841) | 482,748 (35,316) | 779,854 (72,207) |
| Unique reflections | 75,178 (5636) | 78,079 (5561) | 83,520 (5925) | 82,800 (5987) | 60,776 (4265) |
| Multiplicity | 4.7 (3.0) | 6.2 (5.3) | 6.2 (6.2) | 5.8 (5.9) | 12.8 (12.5) |
| Completeness (%) | 94.90 (96.20) | 97.90 (94.90) | 98.10 (94.10) | (99.10) (97.20) | 99.60 (94.50) |
| Mean I/σ(I) | 12.33 (1.60) | 8.54 (2.51) | 10.81 (1.830) | 11.7 (1.77) | 16.01 (1.36) |
| Rsym (%)b | 0.084 (0.943) | 0.127 (0.613) | 0.1057 (0.969) | 0.083 (0.985) | 0.120 (1.341) |
| Rmeas (%)c | 0.095 (1.008) | 0.138 (0.707) | 0.116 (1.078) | 0.091 (0.987) | 0.125 (1.415) |
| Rpim (%)d | 0.042 (0.511) | 0.054 (0.286) | 0.046 (0.418) | 0.037 (0.397) | 0.0348 (0.396) |
| CC1/2 (%)e | 0.999 (0.606) | 0.989 (0.867) | 0.997 (0.682) | 0.998 (0.700) | 0.999 (0.764) |
| Refinement | |||||
| Unique reflections | 75,153 | 78,024 | 83,498 | 82,785 | 60,658 |
| Rworkf | 0.1803 | 0.1993 | 0.1798 | 0.1715 | 0.1836 |
| Rfree | 0.2212 | 0.2381 | 0.2240 | 0.2144 | 0.2208 |
| Protein atoms | 19,795 | 21,296 | 21,129 | 21,512 | 11,736 |
| Ligands atoms | 0 | 234 | 196 | 249 | 145 |
| Solvent atoms | 0 | 41 | 49 | 16 | 135 |
| RMS(bonds) (Å) | 0.003 | 0.005 | 0.002 | 0.006 | 0.002 |
| RMS(angles) (°) | 0.61 | 0.98 | 0.56 | 0.76 | 0.43 |
| Average B-factor (Å2) | |||||
| All atoms | 85.3 | 74.8 | 77.4 | 91.6 | 57.4 |
| Protein | 85.3 | 74.8 | 77.3 | 91.7 | 57.4 |
| Ligand and ions | – | 80.6 | 88.5 | 91.7 | 55.3 |
| Waters | – | 53.0 | 78.1 | 67.5 | 52.2 |
| Ramachandran | |||||
| Favored (%) | 97.73 | 97.16 | 97.05 | 98.84 | 96.81 |
| Allowed (%) | 2.27 | 2.84 | 2.87 | 1.16 | 3.19 |
| Outliers (%) | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 |
| Rotamer outliers (%) | 1.78 | 1.93 | 2.62 | 1.29 | 1.33 |
Highest resolution shell is shown in parentheses.
Rsym/merge = ΣhklΣi|Ii(hkl) − <I(hkl)>|/ΣhklΣiIi(hkl).
Rmeas = Σhkl[N/(N − 1)]1/2Σi|Ii(hkl) − <I(hkl)>|/ΣhklΣiIi(hkl).
Rpim = Σhkl[1/(N − 1)]1/2Σi|Ii(hkl) − <I(hkl)>|/ΣhklΣiIi(hkl) where Ii(hkl), <I(hkl)>, and N represent the intensity measurement, the mean intensity, and the redundancy for reflection hkl, respectively.
CC∗ = [2CC1/2/(1 + CC1/2)]1/2 where CC1/2 is the correlation between two random halves of the datasets, each containing half of the measured intensities for each unique reflection, and CC∗ is an approximation of the correlation coefficient for a noise-free dataset.
Rwork = Σ|Fobs(hkl) − Fcalc(hkl)|/Σ|Fobs(hkl)|, where Fobs(hkl) and Fcalc(hkl) are the observed and calculated structure factor amplitudes of 95% of the reflections used for refinement. Rfree was calculated from the 5% of total reflections that were omitted from the refinement.