Statistics of x-ray diffraction data and structure refinement
| . | PECAM-1 D1-D2 . | ||
|---|---|---|---|
| Native . | Se SAD (single) . | Se SAD (combined) . | |
| Data collection | |||
| Space group | I4122 | I4122 | I4122 |
| Unit cell | |||
| a, b, c, Å | 103.6, 103.6, 286.1 | 104.0, 104.0, 281.8 | 103.6, 103.6, 280.3 |
| α, β, γ, ° | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Wavelength, Å | 0.97872 | 0.97624 | 0.97624 |
| Resolution, Å* | 20-3.0 (3.5-3.0) | 20.0-2.8 (3.2-2.8) | 20-3.0 (3.2-3.0) |
| Rmerge,† (%)* | 19.5 (50.5) | 12.5 (49.3) | 48.3 (79.6) |
| No. of reflections, measured/unique | 177 694/29 711 | 223 739/36 261 | 4 827 647/16 005 |
| <I/σI>* | 8.7 (2.3) | 11.8 (2.4) | 36.3 (8.5) |
| Completeness (%)* | 99.6 (99.8) | 99.6 (99.8) | 98.9 (94.8) |
| Redundancy* | 6.0 (4.7) | 6.2 (4.8) | 301.6 (232.7) |
| Refinement | |||
| Resolution, Å | 20.0-2.80 | ||
| Unique reflections, work/free | 36 246/1 014 | ||
| Rwork/Rfree‡ | 0.238/0.279 | ||
| No. of atoms: protein/carbohydrates/water | 3 232/109/27 | ||
| Molecules/asymmetric unit | 2 | ||
| RMSD from ideal | |||
| Bond lengths, Å | 0.015 | ||
| Bond angles, ° | 1.736 | ||
| Ramachandran plot: favored/allowed/outliers, % | 94.2/5.5/0.3 | ||
| PDB accession no. | 5C14 | ||
| . | PECAM-1 D1-D2 . | ||
|---|---|---|---|
| Native . | Se SAD (single) . | Se SAD (combined) . | |
| Data collection | |||
| Space group | I4122 | I4122 | I4122 |
| Unit cell | |||
| a, b, c, Å | 103.6, 103.6, 286.1 | 104.0, 104.0, 281.8 | 103.6, 103.6, 280.3 |
| α, β, γ, ° | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Wavelength, Å | 0.97872 | 0.97624 | 0.97624 |
| Resolution, Å* | 20-3.0 (3.5-3.0) | 20.0-2.8 (3.2-2.8) | 20-3.0 (3.2-3.0) |
| Rmerge,† (%)* | 19.5 (50.5) | 12.5 (49.3) | 48.3 (79.6) |
| No. of reflections, measured/unique | 177 694/29 711 | 223 739/36 261 | 4 827 647/16 005 |
| <I/σI>* | 8.7 (2.3) | 11.8 (2.4) | 36.3 (8.5) |
| Completeness (%)* | 99.6 (99.8) | 99.6 (99.8) | 98.9 (94.8) |
| Redundancy* | 6.0 (4.7) | 6.2 (4.8) | 301.6 (232.7) |
| Refinement | |||
| Resolution, Å | 20.0-2.80 | ||
| Unique reflections, work/free | 36 246/1 014 | ||
| Rwork/Rfree‡ | 0.238/0.279 | ||
| No. of atoms: protein/carbohydrates/water | 3 232/109/27 | ||
| Molecules/asymmetric unit | 2 | ||
| RMSD from ideal | |||
| Bond lengths, Å | 0.015 | ||
| Bond angles, ° | 1.736 | ||
| Ramachandran plot: favored/allowed/outliers, % | 94.2/5.5/0.3 | ||
| PDB accession no. | 5C14 | ||
PDB, Protein Data Bank; RMSD, root-mean-square deviation.
The highest resolution shell is shown in parentheses.
Rmerge = ΣhΣi|Ii−〈I〉|/ΣhΣiIi, where Ii is the observed intensity of the i-th measurement of reflection h, and〈I〉is the average intensity of that reflection obtained from multiple observations.
R = Σ||Fo|−|Fc||/Σ|Fo|, where Fo and Fc are the observed and calculated structure factors, respectively, calculated for all data. Rfree is the R value obtained for a test set of reflections consisting of a randomly selected 2.8% subset of data excluded from refinement.