Crystallographic data summary for the cocrystal structure of SPPARγM2 with human PPARγLBD
Data Collection | Measurement |
|---|---|
| Space group | C2 |
| Unit cell dimensions | a = 92.15 Å, b = 58.86 Å, c = 118.29 Å, β= 103.76° |
| No. of molecules per asymmetric unit | Two monomers |
| Resolution range (Å) | 50.0-2.25 (2.35-2.25) |
| No. of observations | 181,947 |
| No. of unique reflectionsa | 29,681 (3407) |
| I/σ(I) | 15.5 (2.51) |
| Completeness (%) | 99.0 (93.7) |
| Rsym (%)b | 0.042 (0.353) |
| Structure refinement | |
| Resolution range (Å) | 40.34-2.25 (2.39-2.25) |
| Rcryst/Rfree (%)c | 0.232/0.274 (0.324/0.383) |
| Protein atoms | 3792 |
| Water molecules | 93 |
| Ligand atoms | 88 |
| B-factor from Wilson plot (Å2) | 29.6 |
| Average B-factor for all atoms (Å2) | 43.5 |
| Cross-validated estimated coordinate error (Å)d | 0.37 |
| Root-mean-square deviation from expected geometrye | |
| Bond length (Å) | 0.006 |
| Bond angle (degrees) | 0.9 |
| Dihedral angle (degrees) | 20.6 |
| Improper angle (degrees) | 0.66 |
| Ramachandran statistics | |
| Residues in most favored regions (%) | 91.9 |
| Residues in additional allowed regions (%) | 7.6 |
| Residues in generously allowed region (%) | 0.2 |
| Residues in disallowed region (%) | 0.2 |
↵ a A control set of 5% of these reflections, chosen randomly, were used to calculate an Rfree to monitor the progress of refinement.
↵ b Rsym = Σj | <Ii> - Iij| / ΣiΣj<Ii>, where <Ii> is the mean intensity of the ith reflection, and Iij is the symmetry related jth measurement of the ith reflection.
↵ c Rcryst = Σ | | Fobs | - | Fcalc | | / Σ | Fobs |, where | Fobs | and | Fcalc | are the calculated and observed structure factor amplitudes, respectively, for the 95% of reflections used in refinement. Rfree is calculated in the same manner using only the control set of reflections.
↵ d Luzzati48 method was used along with the control set of reflections used to calculate Rfree.
↵ e Engh and Huber49 stereochemical parameters were used in the refinement.