9PGQ
Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (Apo, trigonal form)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS-II BEAMLINE 19-ID |
| Synchrotron site | NSLS-II |
| Beamline | 19-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2025-04-25 |
| Detector | DECTRIS EIGER2 XE 9M |
| Wavelength(s) | 0.9786 |
| Spacegroup name | P 31 2 1 |
| Unit cell lengths | 83.461, 83.461, 166.173 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 43.970 - 1.500 |
| R-factor | 0.1636 |
| Rwork | 0.163 |
| R-free | 0.18560 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.057 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX ((2.0_5750: ???)) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 43.970 | 1.530 |
| High resolution limit [Å] | 1.500 | 1.500 |
| Rmerge | 0.108 | 2.386 |
| Rmeas | 0.111 | 2.445 |
| Rpim | 0.025 | 0.533 |
| Total number of observations | 2177860 | 109904 |
| Number of reflections | 107896 | 5248 |
| <I/σ(I)> | 17.7 | 1.6 |
| Completeness [%] | 100.0 | |
| Redundancy | 20.2 | 20.9 |
| CC(1/2) | 1.000 | 0.376 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | Index H1: 100 mM Tris, pH 8.5, 200 mM MgCl2, 25% (w/v) PEG 3350. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD and D-glyceraldehyde-3-phosphate added to the protein prior to crystallization but no electron density for the ligands was observed. plate 19840 well H1 drop 3 , Puck: PSL-2105, Cryo: 80% crystallant + 20% PEG 200 |
