Rerefined αIIbβ3 complex x-ray diffraction and refinement data
| Ligand . | Native1 . | Native2 . | Tirofiban . | Eptifibatide . | L-739758 . |
|---|---|---|---|---|---|
| Space group | P3221 | P3221 | P3221 | P3221 | P3221 |
| Unit cell (a, b, c) (Å) | 148.9, 148.9, 176.1 | 148.9, 148.9, 176.4 | 148.6, 148.6, 177.2 | 149.6, 149.6, 175.7 | 149.2, 149.2, 176.2 |
| α, β, γ (degree) | 90, 90, 120 | 90, 90,120 | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 |
| Wavelength (Å) | 0.9793 | 0.9793 | 0.9760 | 0.9760 | 0.9793 |
| Resolution (Å) | 50–2.8 | 50–2.75 | 50–2.9 | 50–2.9 | 50–3.1 |
| Number of reflections (total/unique) | 400,460/55,875 | 442,121/62,512 | 330,745/50,662 | 357,439/50,647 | 263,308/41,586 |
| Completeness (%) | 99.9/99.8b | 99.9/100b | 99.7/98.2b | 100/100b | 99.8/99.7b |
| I/σ (I) | 14.0/3.1b | 20.0/3.0b | 12.1/2.0b | 14.9/2.7b | 12.1/2.7b |
| Rmerge (%) | 13.0/68.1b | 9.6/59.8b | 13.9/57.8b | 11.7/61.5b | 14.0/55.8b |
| Number of atoms (protein/water/other) | 10,404/612/210 | 10,461/1,129/210 | 10,363/355/235 | 10,385/364/223 | 10,348/98/240 |
| Rmsd bond lengths (Å) | 0.005 | 0.006 | 0.005 | 0.005 | 0.007 |
| Rmsd bond angles (degree) | 0.9 | 1.0 | 0.9 | 0.9 | 1.0 |
| Rwork (%) | 16.1 | 14.4 | 16.7 | 16.3 | 18.1 |
| Rfree (%) | 20.4 | 19.1 | 20.6 | 21.3 | 22.0 |
| Ramachandran statistics (% favored/allowed/outlier)a | 97.3/2.5/0.2 | 97.2/2.5/0.3 | 96.5/3.3/0.2 | 96.8/2.9/0.2 | 96.5/3.3/0.2 |
| Obsolete PDB code | 1TY3 | 1TXV | 1TY5 | 1TY6 | 1TY7 |
| New PDB code | 2VDK | 2VDL | 2VDM | 2VDN | 2VC2 |
| Ligand . | Native1 . | Native2 . | Tirofiban . | Eptifibatide . | L-739758 . |
|---|---|---|---|---|---|
| Space group | P3221 | P3221 | P3221 | P3221 | P3221 |
| Unit cell (a, b, c) (Å) | 148.9, 148.9, 176.1 | 148.9, 148.9, 176.4 | 148.6, 148.6, 177.2 | 149.6, 149.6, 175.7 | 149.2, 149.2, 176.2 |
| α, β, γ (degree) | 90, 90, 120 | 90, 90,120 | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 |
| Wavelength (Å) | 0.9793 | 0.9793 | 0.9760 | 0.9760 | 0.9793 |
| Resolution (Å) | 50–2.8 | 50–2.75 | 50–2.9 | 50–2.9 | 50–3.1 |
| Number of reflections (total/unique) | 400,460/55,875 | 442,121/62,512 | 330,745/50,662 | 357,439/50,647 | 263,308/41,586 |
| Completeness (%) | 99.9/99.8b | 99.9/100b | 99.7/98.2b | 100/100b | 99.8/99.7b |
| I/σ (I) | 14.0/3.1b | 20.0/3.0b | 12.1/2.0b | 14.9/2.7b | 12.1/2.7b |
| Rmerge (%) | 13.0/68.1b | 9.6/59.8b | 13.9/57.8b | 11.7/61.5b | 14.0/55.8b |
| Number of atoms (protein/water/other) | 10,404/612/210 | 10,461/1,129/210 | 10,363/355/235 | 10,385/364/223 | 10,348/98/240 |
| Rmsd bond lengths (Å) | 0.005 | 0.006 | 0.005 | 0.005 | 0.007 |
| Rmsd bond angles (degree) | 0.9 | 1.0 | 0.9 | 0.9 | 1.0 |
| Rwork (%) | 16.1 | 14.4 | 16.7 | 16.3 | 18.1 |
| Rfree (%) | 20.4 | 19.1 | 20.6 | 21.3 | 22.0 |
| Ramachandran statistics (% favored/allowed/outlier)a | 97.3/2.5/0.2 | 97.2/2.5/0.3 | 96.5/3.3/0.2 | 96.8/2.9/0.2 | 96.5/3.3/0.2 |
| Obsolete PDB code | 1TY3 | 1TXV | 1TY5 | 1TY6 | 1TY7 |
| New PDB code | 2VDK | 2VDL | 2VDM | 2VDN | 2VC2 |
Rmerge = ΣH Σi |Ii(h) − <I(h)>|/ΣHΣi Ii(h), where Ii(h) and <I(h)> are the ith and mean measurement of the intensity of reflection, h. Rwork = ΣH||Fobs (h)| − |Fcalc (h)||/ΣH|Fobs (h)|, where Fobs (h) and Fcalc (h) are the observed and calculated structure factors, respectively. No I/σ cutoff was applied. Rfree is the R value obtained for a test set of reflections consisting of a randomly selected 5% subset of the data set excluded from refinement.
Determined with RAMPAGE (Lovell et al., 2003).
These numbers correspond to the last resolution shell.