Table 2. Summary of SAXS structural parameters.
| Commd1 | Commd7 | Commd9 | |
|---|---|---|---|
| Data collection parameters | |||
| Instrument | Australian Synchrotron SAXS/WAXS beamline with Dectris PILATUS 1M detector |
||
| Wavelength (Å) | 1.0332 | ||
| Beam geometry (μM) | 250 × 130 | ||
| Camera length (m) | 1.6 | ||
| q-range (Å−1) | 0.011–0.251 | ||
| Absolute scaling method | Comparision with scattering from 1 mm H2O | ||
| Normalization | To transmitted intensity by beam-stop counter | ||
| Method for monitoring radiation damage | Dose maintained below 210 Gy | ||
| Exposure per frame (s) | 1 | ||
| Sample temperature (K) | 283 | ||
| Sample configuration | SEC-SAXS with sheath-flow cell | ||
| Flow-rate (ml/min) | 0.25 | ||
| Structural parameters | |||
| Guinier analysis | |||
| I(0) (cm−1) | 0.04 ± 0.00 | 0.03 ± 0.00 | 0.02 ± 0.00 |
| Rg (Å) | 29.26 ± 0.25 | 28.86 ± 0.60 | 27.61 ± 0.79 |
| qmin (Å−1) | 0.01 | 0.01 | 0.01 |
| qRg max (Å−1) | 1.3 | 1.3 | 1.3 |
| P(r) analysis | |||
| I(0) (cm−1) | 0.04 ± 0.0004 | 0.029 ± 0.0003 | 0.02 |
| Rg (Å) | 30.37 ± 0.59 | 29.5 ± 0.53 | 28.26 ± 0.67 |
| Dmax (Å) | 101.47 | 99.47 | 96.99 |
| q range (Å−1) | 0.011–0.251 | 0.011–0.251 | 0.011–0.251 |
| Porod volume (Å−3) | 71951 | 65393 | 67180 |
| Dry volume calculated from sequence (Å−3) | 25848 | 27271 | 26622 |
| Shape model-fitting results | |||
| Gasbor (default paramters, 20 calculations | |||
| q range (Å−1) for fitting | 0.011–0.251 | 0.011–0.251 | 0.011–0.251 |
| Symmetry, anisotropy assumptions | P2, none | P2, none | P2, none |
| NSD (standard deviation) | 0.16 (0.004) | 1.04 (0.55) | |
| χ2 range, CORMAP P values | 0.15–0.20, 0.11 | 0.14–0.17, 0.47 | 0.14–0.15, 0.14 |
| Atomistic modelling | |||
| Crystal structures | PDB entry 2H2M and 6BP6 | PDB entry 4OE9 and 6BP6 | PDB entry 4OE9 and 6BP6 |
| q range for all modelling | 0.011–0.251 | 0.011–0.251 | 0.011–0.251 |
| CRYSOL (with default parameters) | |||
| No constant subtraction | |||
| χ2 | 0.31 | 0.72 | 1.14 |
| Predicted Rg (Å) | 30.85 | 30.54 | 31.88 |
| Vol (Å), Ra (Å), Dro (eÅ−3) | 53643, 1.40, 0.007 | 46010, 1.400, 0.075 | 57201, 1.400, 0.007 |
| FoXS | |||
| χ2, CORMAP P values | 0.52, 0.99 | 0.78, 0.99 | 0.99, 0.93 |
| Predicted Rg (Å) | 30.82 | 29.18 | 31.84 |
| c1,c2 | 1.03, 0.29 | 1.05, 4.0 | 1.04, 1.20 |
| Molecular mass determination | |||
| Estimated MW from Porod volume | 41387 Da | 38094 Da | 39099 Da |
| Calculated MW from MALLS | 40400 Da | 53000 Da | 47800 Da |
| Calculated MW from sequence | 21362 Da (42724 Da for dimer) | 22540 Da (45080 Da for dimer) | 21819 Da (43639 Da for dimer) |
| Software employed | |||
| Primary data reduction | Australian Synchrotron SAXS/WAXS data reduction package (Scatterbrain) |
||
| Data Processing | PRIMUS and GNOM | ||
| Ab initio modeling | GASBOR | ||
| Validation and averaging | DAMAVER | ||
| Computation of models | SASREF | ||
| Envelope representations | PyMOL | ||