X-ray data collection, refinement statistics, and model analysis for the Bz α-thrombin·FVa2 complex
| Summary . | |
|---|---|
| Data collection | |
| X-ray source | ESRF ID23-2 |
| Wavelength, Å | 0.8726 |
| Space group | P1 |
| Cell constants | a = 62.24 Å, b = 68.23 Å, c = 98.97 Å; α = 72.57°, β = 84.05°, γ = 80.45° |
| Resolution (outer shell, Å) | 64.42-2.55 (2.69-2.55) |
| Total number of observations | 170 648 (24 763) |
| Number of unique reflections | 47 172 (6841) |
| I/σ(I) | 10.8 (2.7) |
| Completeness (%) | 94.6 (94.1) |
| Redundancy | 3.6 (3.6) |
| Rmerge* (%) | 8.0 (42.6) |
| Refinement and model analysis | |
| Resolution (outer shell, Å) | 61.28-2.550 (2.616-2.550) |
| Rfactor† (%) | 20.68 (27.30) |
| Rfree‡ (%) | 27.88 (35.90) |
| rmsd bonds, Å | 0.016 |
| rmsd angles, ° | 1.841 |
| Ramachandran plot (favored/allowed), % | 93.50/5.46 |
| Clashscore (all atoms)§ | 18.74 (78th percentile)‖ |
| MolProbity score¶ | 2.86 (53th percentile)‖ |
| Summary . | |
|---|---|
| Data collection | |
| X-ray source | ESRF ID23-2 |
| Wavelength, Å | 0.8726 |
| Space group | P1 |
| Cell constants | a = 62.24 Å, b = 68.23 Å, c = 98.97 Å; α = 72.57°, β = 84.05°, γ = 80.45° |
| Resolution (outer shell, Å) | 64.42-2.55 (2.69-2.55) |
| Total number of observations | 170 648 (24 763) |
| Number of unique reflections | 47 172 (6841) |
| I/σ(I) | 10.8 (2.7) |
| Completeness (%) | 94.6 (94.1) |
| Redundancy | 3.6 (3.6) |
| Rmerge* (%) | 8.0 (42.6) |
| Refinement and model analysis | |
| Resolution (outer shell, Å) | 61.28-2.550 (2.616-2.550) |
| Rfactor† (%) | 20.68 (27.30) |
| Rfree‡ (%) | 27.88 (35.90) |
| rmsd bonds, Å | 0.016 |
| rmsd angles, ° | 1.841 |
| Ramachandran plot (favored/allowed), % | 93.50/5.46 |
| Clashscore (all atoms)§ | 18.74 (78th percentile)‖ |
| MolProbity score¶ | 2.86 (53th percentile)‖ |
Rmerge = ΣĥΣî|I(hî) − <I(h)>|/ΣĥΣîI(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 5% of all 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 (2.55 ± 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.