Table 1.
Statistics of X-ray diffraction and structure refinement of human pro-TGF-β1 R249A mutant (PDB entry 5VQP)
| Pro-TGF-β1 R249A mutant (PDB entry 5VQP) | |
|---|---|
| Data collection statistics | |
| Space group | P 6 2 2 |
| α, β, γ (degrees) | 90, 90, 120 |
| Unit cell (a, b, c), Å | 104.4, 104.4, 141.9 |
| Resolution range (Å) | 50.0–2.9 (3.0–2.9)a |
| Completeness (%) | 99.7 (99.9)a |
| No. of unique reflections | 10,672 (1,024)a |
| Redundancy | 10.5 (10.9)a |
| Rmergeb (%) | 17.1 (601)a |
| I/σ | 12.3 (0.5)a |
| CC½ (%)c | 99.9 (15.1)a |
| Wavelength (Å) | 1.0332 |
| Refinement statistics | |
| Rworkd (%) | 25.2 (41.3)a |
| Rfreee (%) | 29.3 (42.3)a |
| Bond RMSD (Å) | 0.004 |
| Angle RMSD (degrees) | 0.64 |
| Ramachandran plotf (favored/allowed/outlier) | 95.5/4.5/0 |
| MolProbity percentilef (Clashscore/geometry) | 96/99 |
| No. of atoms | |
| Protein | 2576 |
| Carbohydrates | 39 |
| No. of cis-prolines | 1 |
| B-factors | |
| Protein | 127.0 |
| Carbohydrates | 221.8 |
a Numbers in parentheses are for the highest-resolution shell.
b 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.
c Pearson's correlation coefficient between average intensities of random half-data sets for unique reflections (34).
d 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(I) cutoff was applied.
e Rfree is the R value obtained for a test set of reflections consisting of a randomly selected ∼3% subset of the data set excluded from refinement.
f Calculated with MolProbity (22).