Table 1.
Crystallographic data for the structures of human beta-2 glycoprotein I
| Parameter | Value(s) for: |
||
|---|---|---|---|
| pβ2GPI | hrβ2GPI | ST-β2GPI | |
| Buffer/salt | 100 mm HEPES, pH 7.5/1.5 m AmSO4, 20 mm CaCl2, 2% glycerol | 100 mm MES, pH 6.0/1.6 m AmSO4 | 100 mm HEPES, pH 7.5/1.5 m AmSO4, 20 mm CaCl2, 2% glycerol |
| PDB entry | 6V06 | 6V08 | 6V09 |
| Data collection | |||
| Wavelength (Å) | 1.54 | 1.033 | 1.54 |
| Space group | C2221 | C2221 | C2221 |
| Unit cell dimensions (Å) | a = 160.8, b = 166.9, c = 114.0 | a = 159.3, b = 173.2, c = 115.2 | a = 160.2, b = 171.2, c = 113.4 |
| Molecules/asymmetric unit | 1 | 1 | 1 |
| Resolution range (Å) | 40–2.4 | 40–2.6 | 40–3.0 |
| No. of observations | 513,296 | 363,697 | 158,386 |
| No. of unique observations | 59,497 | 48,503 | 31,543 |
| Completeness (%) | 98.8 (97.1) | 97.1 (77.1) | 98.8 (97.7) |
| Rsym (%) | 7.9 (50.6) | 14.3 (64.7) | 9.5 (46.1) |
| I/σ(I) | 21.1 (2.4) | 10.0 (1.5) | 13.7 (2.4) |
| Refinement | |||
| Resolution (Å) | 40–2.4 | 40–2.6 | 40–3.0 |
| Rcryst, Rfree | 0.201, 0.236 | 0.200, 0.232 | 0.223, 0.246 |
| No. of reflections (working/test) | 56,556/2935 | 45,862/2599 | 29,924/1611 |
| No. of protein atoms | 2540 | 2510 | 2517 |
| No. of solvent molecules | 431 | 377 | 15 |
| RMSDa bond lengths (Å) | 0.013 | 0.010 | 0.011 |
| RMSD angles (˚) | 2.0 | 2.0 | 1.7 |
| RMSD ΔB (Å2) (mm/ms/ssb) | 5.12/5.28/6.93 | 4.54/5.13/5.85 | 3.97/3.58/4.38 |
| Protein (Å2) | 63.8 | 68.5 | 71.0 |
| Solvent (Å2) | 64.4 | 62.8 | 49.6 |
| Ramachandran plot: | |||
| Most favored (%) | 98.9 | 100.0 | 99.6 |
| Generously allowed (%) | 1.1 | 0.0 | 0.4 |
| Disallowed (%) | 0.0 | 0.0 | 0.0 |
aRMSD from ideal bond lengths and angles and RMSD in B-factors of bonded atoms.
bmm, main chain–main chain; ms, main chain–side chain; ss, side chain–side chain.