9DIE
Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | LIQUID ANODE |
| Source details | BRUKER METALJET |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-05-04 |
| Detector | Bruker PHOTON III |
| Wavelength(s) | 1.34138 |
| Spacegroup name | I 1 2 1 |
| Unit cell lengths | 79.999, 105.327, 108.406 |
| Unit cell angles | 90.00, 93.83, 90.00 |
Refinement procedure
| Resolution | 24.430 - 1.850 |
| R-factor | 0.12119 |
| Rwork | 0.119 |
| R-free | 0.16740 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.766 |
| Data reduction software | PROTEUM2 (2021.10-0) |
| Data scaling software | Aimless (0.7.9) |
| Phasing software | MOLREP (11.9.12) |
| Refinement software | REFMAC (5.8.0425) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 24.430 | 1.890 |
| High resolution limit [Å] | 1.850 | 1.850 |
| Rmerge | 0.167 | 1.836 |
| Number of reflections | 76317 | 4518 |
| <I/σ(I)> | 9.6 | |
| Completeness [%] | 99.9 | |
| Redundancy | 6.6 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 298 | 1 mg/mL protein, 0.4 mM ceramidephosphoethanolamine, 5 mg/mL CHAPS, 8.25% methyl-2,4-pentanediol, 75 mM sodium chloride, 27.5 mM sodium acetate (pH 4.6), ~30 mM Tris, 1 mM magnesium chloride |
