9HDE
Crystal structure of methionine gamma-lyase (K209Q variant) from Brevibacterium aurantiacum in complex with PLP and alpha-ketobutyrate
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SOLEIL BEAMLINE PROXIMA 2 |
| Synchrotron site | SOLEIL |
| Beamline | PROXIMA 2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-03-29 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.98399 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 133.328, 155.890, 232.079 |
| Unit cell angles | 90.00, 90.24, 90.00 |
Refinement procedure
| Resolution | 232.080 - 2.522 |
| R-factor | 0.2581 |
| Rwork | 0.258 |
| R-free | 0.26520 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.008 |
| RMSD bond angle | 0.960 |
| Data reduction software | XDS (Jan 10, 2022) |
| Data scaling software | Aimless (0.7.7) |
| Phasing software | PHASER (2.7) |
| Refinement software | BUSTER (2.10.4) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 232.077 | 232.077 | 2.820 |
| High resolution limit [Å] | 2.522 | 7.857 | 2.522 |
| Rmerge | 0.322 | 0.068 | 1.219 |
| Rmeas | 0.350 | 0.074 | 1.326 |
| Rpim | 0.136 | 0.029 | 0.516 |
| Total number of observations | 1354142 | 67536 | 67155 |
| Number of reflections | 214191 | 10709 | 10710 |
| <I/σ(I)> | 5.9 | 16.72 | 1.63 |
| Completeness [%] | 93.6 | 99.2 | 61.6 |
| Completeness (spherical) [%] | 67.2 | 99.2 | 11.9 |
| Completeness (ellipsoidal) [%] | 93.6 | 99.2 | 61.6 |
| Redundancy | 6.32 | 6.31 | 6.27 |
| CC(1/2) | 0.980 | 0.996 | 0.440 |
| Anomalous completeness (spherical) | 66.5 | 97.8 | 11.5 |
| Anomalous completeness | 93.2 | 97.8 | 61.5 |
| Anomalous redundancy | 3.2 | 3.3 | 3.2 |
| CC(ano) | -0.043 | -0.324 | -0.009 |
| |DANO|/σ(DANO) | 0.8 | 0.6 | 0.8 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 2.852 Å | 0.905, 0.905, 0.905 |
| 3.152 Å | 0.000, 0.000, 0.000 |
| 2.522 Å | -0.425, -0.425, -0.425 |
| Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 294 | Well solution 0.1 M Tris-HCl, pH 8.5, 0.1 M Lithium sulfate, 32% PEG4000, 1 mM PLP, 20 mM Methionine, Cryoprotection: 10% PEG400 |
