Table 1. Crystallographic data collection and refinement statistics.
Rab8A:GDP | Rab8A:GppNHp | |
---|---|---|
Crystal parameters | ||
Space group | C2 | P21 |
Cell constants |
a = 117.6 Å; b = 75.2 Å; c = 107.7 Å; β = 100.5 Å |
a = 34.9 Å; b = 93.7 Å; c = 56.1 Å; β = 103.0 Å |
Subunits/AU1 | 5 | 2 |
Data collection | ||
Beam line | X06SA, SLS | X06SA, SLS |
Wavelength (Å) | 1.0 | 1.0 |
Resolution range (Å)2 | 50–2.4 (2.5–2.4) | 50–2.5 (2.6–2.5) |
No. observed reflections | 105 949 | 35 644 |
No. unique reflections3 | 35 267 | 11 734 |
Completeness (%)2 | 97.2 (96.9) | 95.9 (92.3) |
Rmerge (%)2,4 | 0.096 (0.574) | 0.123 (0.578) |
I/σ (I)2 | 9.5 (2.1) | 6.5 (2.0) |
Refinement (REFMAC5) | ||
Resolution range (Å) | 30–2.4 | 30–2.5 |
No. refl. working set | 33 488 | 11 143 |
No. refl. test set | 1763 | 586 |
No. non hydrogen | 6875 | 2845 |
No. of pSer111 | 5 | 2 |
No. of Mg2+ | 5 | 2 |
No. of nucleotide | 5 | 2 |
Solvent | 45 | 17 |
Rwork/Rfree (%)5 | 23.3/26.2 | 24.3/27.8 |
r.m.s.d. bond (Å)/(°)6 | 0.002/1.2 | 0.002/1.2 |
Average B-factor (Å2) | 48.4 | 51.8 |
pSer111 | 89.7 | 55.1 |
Nucleotide | 40.2 | 43.4 |
Ramachandran plot (%)7 | 97.8/2.2/0 | 98.5/1.5/0 |
PDB accession code | 6STF | 6STG |
Asymmetric unit;
The values in parentheses for resolution range, completeness, Rmerge and I/σ(I) correspond to the highest resolution shell;
Data reduction was carried out with XDS. Friedel pairs were treated as identical reflections;
Rmerge(I) = ΣhklΣj | I(hkl)j − <I(hkl)> | / Σhkl Σj I(hkl)j, where I(hkl)j is the jth measurement of the intensity of reflection hkl and <I(hkl)> is the average intensity;
R = Σhkl | |Fobs| − |Fcalc| |/Σhkl |Fobs|, where Rfree is calculated for a randomly chosen 5% of reflections, which were not used for structure refinement, and Rwork is calculated for the remaining reflections;
Deviations from ideal bond lengths/angles;
Percentage of residues in favoured/allowed/outlier region.