Table 2.
X-ray data collection, refinement statistics, and model analysis for the FPR–α-thrombin·FVa2 complex
| Summary | |
|---|---|
| Data collection | |
| X-ray source | ESRF ID23-1 |
| Wavelength, Å | 0.9725 |
| Space group | P1 |
| Cell constants | a = 52.21 Å, b = 62.26 Å, c = 67.51 Å; α = 99.38°, β = 110.46°, γ = 92.26° |
| Resolution (outer shell, Å) | 62.14-1.69 (1.79-1.69) |
| Total number of observations | 268 275 (38 322) |
| Number of unique reflections | 81 788 (11 372) |
| I/σ(I) | 12.3 (2.4) |
| Completeness (%) | 94.2 (89.6) |
| Redundancy | 3.3 (3.4) |
| Rmerge* (%) | 8.4 (38.6) |
| Refinement and model analysis | |
| Resolution (outer shell, Å) | 31.92-1.696 (1.740-1.696) |
| Rfactor† (%) | 19.96 (36.90) |
| Rfree‡ (%) | 23.88 (41.60) |
| rmsd bonds, Å | 0.023 |
| rmsd angles, ° | 2.032 |
| Ramachandran plot (favored/allowed), % | 97.02/2.98 |
| Clashscore (all atoms)§ | 11.80 (58th percentile)‖ |
| MolProbity score¶ | 2.13 (44th percentile)‖ |
Rmerge = ΣĥΣî|I(hî) − <I(h)>|/ΣĥΣî I(hî), where I(hî) is the intensity of the hth reflection as determined by the ith measurement, and <I(h)> is the average value.
Rfactor = Σ(|Fobs| − |Fcalc|)/Σ|Fobs|, where |Fobs| and |Fcalc| are observed and calculated structure factor amplitudes, respectively.
Rfree: Rfactor calculated for a randomly selected test set comprising 2047 reflections (2.5% of all unique reflections), which were excluded from refinement.
Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.
The 100th percentile is the best among structures of comparable resolution (1.70 ± 0.25 Å); 0th percentile is the worst.
MolProbity score is defined as 0.42574*log(1 + clashscore) + 0.32996*log(1 + max(0,%RotOut-1)) + 0.24979*log(1 + max(0,100-%RamaFavored-2)) + 0.5, where %RotOut is the percentage of bad side-chain rotamers and %RamaFavored is the percentage of residues in favored regions of the Ramachandran plot.