Table 1.
Data Collection, Structure Determination, and Refinement Statistics of Human Pds5B Bound to Wapl1–33
| Data collection | |
|---|---|
| Space group | P212121 |
| Cell constants a, b, c (Å) | 120.76, 162.37, 173.06 |
| Wavelength (Å) | 0.97918 |
| Resolution range (Å) | 40.6 – 2.70 (2.75 – 2.70)a |
| Unique reflections | 92,470 (4,540) |
| Multiplicity | 8.1 (6.6) |
| Data completeness (%) | 99.9 (99.4) |
| Rmerge (%)b,c | 9.5 (100) |
| Rpim(%)c,d | 4.7 (76.5) |
| I/σ(I) | 18.4 (1.2) |
| Wilson B-value (Å2) | 38.1 |
| Phase determination | |
| Anomalous scatterers | Se, 73 out of 66 possible sites |
| Refinement statistics | |
| Resolution range (Å) | 40.6 – 2.71 (2.78 – 2.71) |
| No. of reflections Rwork/Rfree | 81,101/1,991 (2,181/61) |
| Data completeness (%) | 87.4 (34.0) |
| Atoms (non-H protein/peptide/IP6) | 17,387/45/72 |
| Rwork (%) | 21.6 (32.9) |
| Rfree (%) | 25.3 (43.3) |
| R.m.s.d. bond length (Å) | 0.003 |
| R.m.s.d. bond angle (°) | 0.62 |
| Mean B-value (Å2) (protein, chain A/IP6, chain A/protein, chain B/IP6, chain B/peptide, chain C) | 41.4/33.4/63.4/46.4/91.6 |
| Ramachandran plot (%) (favored/additional/disallowed)e | 97.2/2.6/0.2 |
| Missing residues | A: 589–594, 1102–1107, 1117–1120. B: 46–48, 91–94, 539–543, 587–595, 1101–1107. C: 1–6, 12–33. |
a
Data for the outermost shell are given in parentheses.
b
Rmerge = 100 ΣhΣi|Ih,i—〈Ih〉|/ΣhΣi 〈Ih,i〉, where the outer sum (h) is over the unique reflections and the inner sum (i) is over the set of independent observations of each unique reflection.
c
Bijvoet-pairs were kept separate for data processing.
d
Rpim = 100 ΣhΣi [1/(nh − 1)]1/2|Ih,i—〈Ih〉|/ΣhΣi 〈Ih,i〉, where nh is the number of observations of reflections h (Evans, 2011).
e
As defined by the validation suite MolProbity (Chen et al., 2010).