Table 1.
SeMet Combined Dataset 1a | SeMet Combined Dataset 2b | Nativec | ||||
---|---|---|---|---|---|---|
Space group | P6122 | P6122 | P6122 | |||
Cell dimensions | ||||||
a, b, c (Å) | 119.27, 119.27, 551.68 | 119.39, 119.39, 551.86 | 119.34, 119.34, 551.98 | |||
α, β, γ (°) | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 | |||
Mosaicity (°) | 0.44 | 0.46 | 0.49 | |||
overall | highest shell | overall | highest shell | overall | highest shell | |
Wavelength (Å) | 0.97918 | 0.97918 | 0.97918 | |||
Beam/detector | 24-ID-C | Pilatus 6M-F | 24-ID-C | Pilatus 6M-F | 24-ID-E | Eiger 16M |
Observations | 3,925,944 | 104,010 | 5,907,898 | 227,087 | 770,154 | 50,223 |
Unique reflections | 69,991 | 4,232 | 68,911 | 2,776 | 48,607 | 4,315 |
Resolution (Å) | 62.66–2.64 | 2.7–2.64 | 68.72–2.59 | 2.65–2.59 | 96.79–2.99 | 3.09–2.99 |
Rmerged | 0.414 | 6.203 | 0.251 | 1.655 | 0.326 | 2.76 |
Rmease | 0.418 | 6.334 | 0.253 | 1.666 | 0.336 | 2.89 |
Rpimf | 0.058 | 1.27 | 0.027 | 0.18 | 0.083 | 0.83 |
I/σ(I) | 12.5 | 1.1 | 22.9 | 5.6 | 9.6 | 1.1 |
CC1/2 | 0.994 | 0.251 | 0.998 | 0.646 | 0.983 | 0.224 |
Completeness | 99.7 | 95.6 | 93.7 | 60.5 | 100 | 99.9 |
Multiplicity | 56.1 | 24.6 | 85.7 | 81.8 | 15.8 | 11.6 |
Refinement | PDB: ID 6MO6 | PDB: ID 6MP5 | ||||
Rwork/Rfree | 0.187/0.245 | 0.208/0.264 | ||||
No. of atoms | ||||||
Overall | 13,533 | 13,260 | ||||
Protein | 13,040 | 13,020 | ||||
Ligands | 216 | 212 | ||||
Waters | 277 | 28 | ||||
RMSD from ideality | ||||||
Bonds (Å) | 0.004 | 0.003 | ||||
Angles (°) | 0.98 | 0.605 | ||||
B factors (Å2) | ||||||
Mean | 39.6 | 69.2 | ||||
Protein | 39.7 | 69.4 | ||||
Ligands | 33.9 | 61.1 | ||||
Waters | 35.8 | 54.1 |
SeMet combined dataset 1 was produced by combining datasets collected with two crystals of SeMet-substituted enzyme, crystal A and crystal B, at a detector distance of 400 and 440 mm, respectively. Crystal A was grown using the condition 20% glycerol, 7.8% PEG 4K, 0.1 M sodium acetate trihydrate pH 4.6, 0.32 M ammonium acetate, 0.1% DHPC, 0.31 mM DCQ, and 10 mM N-ethylmaleimide. Crystal B was grown using the condition 20% glycerol, 8.2% PEG 4K, 0.1 M sodium acetate trihydrate pH 4.6, 0.32 M ammonium acetate, 0.1% DHPC, 0.31 mM DCQ, and 10 mM thiosulfate pentahydrate.
SeMet combined dataset 2 was produced by combining two datasets collected from different positions within with crystal B.
Native dataset was collected at a detector distance of 500 mm from a single crystal of native enzyme grown in 10% glycerol, 14% PEG 4K, 0.1 M sodium acetate trihydrate pH 4.6, 0.5 M ammonium acetate, and 0.1% DHPC.
Rmerge = ΣhklΣi|Ihk,i − 〈Ihkl〉|/Σhkl〈Ihkl〉.
Rmeas = Σhkl[N/(−1)]½ Σi|Ii(hkl) − 〈I(hkl)〉|/Σhkl Σi Ii(hkl).
Rp.i.m. = Σhkl[1/(−1)]½ Σi|Ii(hkl) − 〈I(hkl)〉|/Σhkl Σi Ii(hkl).