TABLE 1.
Summary of crystallographic dataa
| Data collection statistics | VxrA-SD_1 | VxrA-SD_2 | VxrA-SDΔN239 | VxrA-SDΔN239-T240 | VxrA-SDΔD238-T240 |
|---|---|---|---|---|---|
| Space group | P41212 | P212121 | P41212 | P41212 | P1 |
| Unit cell dimensions | |||||
| a, b, c (Å) | 88.60, 88.60, 107.0 | 112.1, 116.7, 120.7 | 87.65, 87.65, 106.2 | 87.86, 87.86, 107.7 | 45.59, 51.10, 65.63 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 76.11, 73.53, 88.56 |
| Mol wt (Da; residue) | 24,585 (219)b | 24,585 (219)b | 24,472 (218)b | 24,371 (217)b | 24,256 (216)b |
| Mol (AU) | 1 | 4 | 1 | 1 | 2 |
| Se-Met (AU) | 4 | NA | NA | NA | NA |
| Wavelength (Å) | 0.9792 | 0.9792 | 0.9792 | 0.9792 | 0.9792 |
| Resolution limit (Å) | 1.98 | 2.25 | 2.00 | 2.20 | 1.98 |
| No. of unique reflections | 30,252c | 75,884 | 29,036 | 22,071 | 36,860 |
| Rmerge (%) | 9.7 (64.7)d | 5.1 (80.3)e | 7.1 (78.7)f | 8.8 (86.0)g | 9.1 (78.0)h |
| Completeness (%) | 99.8 (100.0)d | 99.6 (99.9)e | 99.9 (99.8)f | 99.8 (99.9)g | 95.9 (92.8)h |
| CC1/2 | 1.00 (0.94)d | 1.00 (0.72)e | 1.00 (0.75)f | 0.98 (0.74)g | 1.00 (0.55)h |
| Redundancy | 11.5 (11.8)d | 4.3 (4.4)e | 8.0 (7.8)f | 5.7 (6.0)g | 3.6 (3.3)h |
| I/σ (I) | 49.8 (4.0)d | 25.9 (1.3)e | 42.2 (2.4)f | 29.3 (1.7)g | 24.4 (1.7)h |
| Solvent content (%) | 70.6 | 69.4 | 70.0f | 70.7 | 57.4 |
| Phasing | |||||
| Resolution range (Å) | 37.2–1.98 | 46.6–3.00 | 45.4–3.00 | 45.9–3.00 | 44.1–3.00 |
| RCullis (anomalous)i (%) | 0.55 | ||||
| FOM before DM | 0.33 | ||||
| Correlation coefficientj (%) | 51.7 | 56.3 | 59.7 | 44.3 | |
| Refinement | |||||
| Resolution range (Å) | 37.2–1.98 | 46.6–2.25 | 45.4–2.00 | 45.9–2.20 | 44.1–1.98 |
| No. of reflections | 30,175 | 75,798 | 28,978 | 21,978 | 36,789 |
| Completeness (%) | 99.7 | 99.4 | 98.7 | 99.8 | 93.1 |
| Rwork/Rfree (%) | 18.4/20.3 | 20.5/22.7 | 18.1/20.9 | 20.2/22.7 | 19.6/24.4 |
| No. of atoms (protein/HETATM) | 1,636/151 | 6,901/236 | 1,769/149 | 1,779/84 | 3,406/136 |
| RMSD | |||||
| Bond length (Å) | 0.006 | 0.002 | 0.017 | 0.003 | 0.010 |
| Bond angle (°) | 1.000 | 0.464 | 1.524 | 0.601 | 1.049 |
| B-factors (Å2) (main/side chain) | 52.5/56.2 | 70.5/72.0 | 45.0/47.9 | 66.2/68.6 | 48.3/53.8 |
| Wilson B-factor (Å2) | 36.8 | 52.5 | 41.3 | 55.6 | 42.1 |
| MolProbity validation | |||||
| Ramachandran outliers (%) | 0.0 | 0.12 | 0.0 | 0.5 | 0.0 |
| Ramachandran favored (%) | 97.6 | 97.5 | 99.5 | 98.2 | 98.4 |
| Rotamer outliners (%) | 1.2 | 1.7 | 3.7 | 4.2 | 1.6 |
| Clashscore | 1.21 | 2.18 | 3.65 | 1.68 | 2.36 |
| MolProbity score | 0.97 | 1.29 | 1.77 | 1.39 | 1.17 |
| PDB ID | 4R7Q | 7KB3 | 7LA6 | 7KB7 | 7KB9 |
a
AU, asymmetric units; RMSD, root mean square deviation.
b
Not including three N-terminal vector-derived residues, SNA.
c
Including Bijvoet pairs.
d
Last resolution bin, 1.98 to 2.01 Å.
e
Last resolution bin, 2.25 to 2.29 Å.
f
Last resolution bin, 2.00 to 2.03 Å.
g
Last resolution bin, 2.20 to 2.24 Å.
h
Last resolution bin, 1.98 to 2.01 Å.
i
Single-wavelength anomalous diffraction (SAD) method.
j
Molecular replacement method.