Table 1 Crystallographic data and refinement statistics.
Dataset (PDB ID) | native (6GS2) | thiomersal | AMPPNP (6H5E) |
|---|---|---|---|
Data collection | |||
X-ray source | SLS X06DA (PXIII) | SLS X10SA (PXII) | SLS X06DA (PXIII) |
X-ray detector | Pilatus 2 M | Pilatus 6 M | Pilatus 2 M |
Wavelength [Å] | 1.0 | 1.0 | 1.0 |
Space group | P212121 | P212121 | P212121 |
Unit cell axes (Å) | a = 107.10 b = 110.37 c = 116.36 | a = 106.97 b = 109.27 c = 116.03 | a = 109.72 b = 109.74 c = 123.30 |
Unic cell angles (°) | α = β = γ = 90 | α = β = γ = 90 | α = β = γ = 90 |
Resolution [Å] | 50–2.04 | 50–2.49 | 50–2.14 |
Reflections (unique) | 641308 (88009) | 1411718 (91196) | 1114473 (82581) |
Redundancy | 7.3 | 13.8 | 13.5 |
Complenteness [%] (last bin) | 99.7 (99.1) | 99.7 (98.1) | 99.8 (98.6) |
I/σ(I) | 14.01 (1.57) | 17.33 (1.88) | 19.37 (1.41) |
Rmeas [%] | 11.2 (178.9) | 3.5 (131.3) | 11.6 (213.0) |
CC1/2 [%] | 99.9 (72.5) | 99.9 (71.2) | 100.0 (67.6) |
Wilson B [Å2] | 40.9 | 56.0 | 51.9 |
SIRAS phasing | |||
Resolution [Å] | 50–2.08 | ||
No. of heavy atoms in ASU | 13 | ||
Phasing power (iso/ano) | |||
centric | 0.898/− | ||
acentric | 0.685/0.382 | ||
FOM | |||
centric | 0.15862 | ||
acentric | 0.14178 | ||
Rcullis (iso/ano) | |||
centric | 0.856/− | ||
acentric | 0.886/0.965 | ||
Refinement | |||
Resolution included [Å] | 49.07–2.04 | 49.08–2.14 | |
Software | PHENIX (1.10.1) | PHENIX (1.10.1) | |
Non-solvent atoms | 9893 | 9909 | |
Solvent atoms | 639 | 442 | |
Rwork/Rfree [%] | 17.5/21.6 | 19.2/23.5 | |
Size of Rfree test set [%] | 1.71 (1503 reflections) | 1.82 (1504 reflections) | |
Bond r.m.s.d. | 0.011 | 0.011 | |
Angle r.m.s.d. | 1.097 | 1.424 | |
Ramachandran [%] (favoured, allowed, outliers*) | 97.43, 2.57, 0.00 | 96.44, 3.48, 0.08 | |
Rotamer outliers [%] | 1.97 | 1.79 | |
All-atom clashscore+ | 3.34 | 5.02 | |
Average B factors [Å2] | 41.3 | 60.2 | |
protein | 41.0 | 60.1 | |
ligand | — | 50.4 | |
ions | 42.8 | 59.3 | |
solvent | 45.6 | 63.8 | |
