TABLE 2.
Data collection and refinement statistics
| Parameter | Valuea |
|||
|---|---|---|---|---|
| VP1 | VP1-3SL | VP1-3SLN | VP1-3GSLN | |
| Data collection statistics | ||||
| Space group | P212121 | P212121 | P212121 | P212121 |
| Unit cell dimensions | ||||
| a, b, c (Å) | 97.33, 180.09, 199.39 | 97.01, 180.40, 199.66 | 96.91, 180.63, 199.42 | 103.40, 177.65, 198.65 |
| α, β, γ (°) | α = β = γ = 90 | α = β = γ = 90 | α = β = γ = 90 | α = β = γ = 90 |
| Resolution (Å) | 50–2.00 (2.05–2.00) | 50–2.09 (2.14–2.09) | 50–2.00 (2.05–2.00) | 50–2.10 (2.15–2.10) |
| Total no. of reflections | 802,267 (58,665) | 645,464 (43,686) | 737,257 (47,697) | 812,743 (62,074) |
| No. of unique reflections | 226,820 (16,603) | 204,785 (14,851) | 230,735 (16,974) | 211,585 (15,585) |
| Redundancy | 3.5 (3.5) | 3.2 (2.9) | 3.2 (2.8) | 3.8 (4.0) |
| 〈I〉/σ〈I〉 | 11.1 (2.1) | 8.4 (1.9) | 10.0 (2.0) | 10.5 (2.2) |
| Completeness (%) | 96.2 (95.9) | 99.0 (97.9) | 98.0 (98.0) | 99.4 (99.6) |
| Rmeas (%) | 11.0 (78.1) | 14.8 (77.9) | 12.4 (75.2) | 15.1 (80.7) |
| Wilson B factor (Å2) | 30.4 | 29.4 | 28.3 | 28.3 |
| Refinement statistics | ||||
| Rwork (%) | 19.6 | 17.8 | 17.9 | 18.4 |
| Rfreeb (%) | 23.6 | 21.6 | 21.3 | 22.4 |
| Coordinate errorc (Å) | 0.26 | 0.25 | 0.24 | 0.25 |
| No. of atoms: | ||||
| Protein | 20,822 | 20,644 | 20,734 | 20,686 |
| Oligosaccharide | 387 | 414 | 470 | |
| Water | 1,885 | 2,364 | 2,523 | 2,395 |
| Othersd | 94 | 182 | 170 | 166 |
| Avg B factors (Å2) | ||||
| Protein atoms | 27.4 | 27.3 | 26.6 | 25.8 |
| Oligosaccharide | 35.8 | 35.2 | 30.2 | |
| Water | 30.9 | 29.9 | 29.1 | 29.3 |
| Othersd | 38.9 | 35.6 | 36.8 | 35.5 |
| RMSD | ||||
| Bond length (Å) | 0.008 | 0.008 | 0.008 | 0.008 |
| Bond angle (°) | 1.26 | 1.23 | 1.21 | 1.22 |
| Ramachandran plote (%) | ||||
| Favorable | 95.76 | 96.10 | 96.32 | 96.07 |
| Allowed | 4.24 | 3.90 | 3.68 | 3.93 |
| Outlier | 0 | 0 | 0 | 0 |
a
Data for the highest-resolution shell are shown in parentheses. A single crystal was used for each data set.
b
Five percent of total reflections were used to calculate Rfree.
c
Coordinate error by Luzzati plot was calculated using the sfcheck program in the CCP4 suite.
d
Others include the substances used for crystallization, i.e., isopropanol, calcium, and ethylene glycol.
e
Calculated using the MolProbity server (http://molprobity.biochem.duke.edu/).