Table 2.
Statistics of X-ray diffraction data collection for CnKBL.
| WT (Ligand-free) | K246A (L-Thr-PLP) | K246A(L-3-HN-PLP) | K246A (Gly-PLP) | |
|---|---|---|---|---|
| Space group | P21 | P21 | P21 | P21 |
| Unit cell parameters | ||||
| a (Å) | 58.38 | 58.71 | 58.73 | 58.69 |
| b (Å) | 105.8 | 101.7 | 101.7 | 101.8 |
| c (Å) | 67.74 | 69.85 | 69.78 | 69.83 |
| α (degree) | 90.0 | 90.0 | 90.0 | 90.0 |
| β (degree) | 105.8 | 113.0 | 112.9 | 113.0 |
| γ (degree) | 90.0 | 90.0 | 90.0 | 90.0 |
| X-ray source | PF BL-5A | PF BL-5A | PF BL-5A | PF BL-5A |
| Wavelength (Å) | 1.00 | 1.00 | 1.00 | 1.00 |
| Resolution (Å) | 41.1-1.80 (1.87-1.80) | 49.9-2.50 (2.58-2.50) | 47.8-2.55 (2.64-2.55) | 47.7-2.50 (2.59-2.50) |
| No. of reflectionsa | 496591 | 269014 | 169899 | 180307 |
| No. of unique reflections | 73094 | 26320 | 24744 | 26198 |
| Completeness (%) | 99.9 (99.5) | 99.8 (98.5) | 99.7 (98.6) | 99.9 (99.7) |
| I/sig (I) | 22.6 (4.5) | 16.3 (4.2) | 13.1 (3.5) | 15.5 (4.1) |
| Rmergeb | 0.049 (0.382) | 0.109 (0.518) | 0.118 (0.516) | 0.104 (0.460) |
| CC1/2 | 0.999 (0.937) | 0.998 (0.904) | 0.996 (0.856) | 0.997 (0.900) |
| B of Wilson plot (Å2) | 20.1 | 28.6 | 24.9 | 23.5 |
| Rc | 0.164 | 0.188 | 0.186 | 0.171 |
| Rfreed | 0.195 | 0.250 | 0.263 | 0.231 |
| Root-mean-square deviation | ||||
| Bond length (Å) | 0.006 | 0.008 | 0.009 | 0.007 |
| Bond angles (deg) | 0.79 | 0.89 | 1.00 | 0.86 |
| Geometry | ||||
| Ramachandran outlier (%) | 0 | 0.13 | 0.76 | 0.13 |
| Ramachandran favored (%) | 97.0 | 95.3 | 94.7 | 95.2 |
| Average B factor (Å2) | 26.6 | 41.3 | 36.5 | 33.8 |
| Protein atoms | 25.5 | 41.5 | 36.8 | 33.9 |
| Ligand atoms | n.d.e | 30.6 | 25.4 | 23.6 |
| Solvent atoms | 34.5 | 37.0 | 32.3 | 31.4 |
| PDB entry | 7BXP | 7BXQ | 7BXR | 7BXS |
aSigma cutoff was set to none (F > 0σF).
bRmerge = ΣhΣi | Ii(h)−<I(h)>|/ Σh I(h), where Ii(h) is the ith measurement of reflection h, and <I(h)> is the mean value of the symmetry-related reflection intensities. Values in brackets are for the shell of the highest resolution.
cR = Σ | | Fo | −|Fc | |/ Σ | Fo | , where Fo and Fc are the observed and calculated structure factors used in the refinement, respectively.
dRfree is the R-factor calculated using 5% of the reflections chosen at random and omitted from the refinement.