9HEE
Crystal structure of methionine gamma-lyase from Brevibacterium aurantiacum having disordered N-terminus and devoid of PLP cofactor
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SOLEIL BEAMLINE PROXIMA 1 |
| Synchrotron site | SOLEIL |
| Beamline | PROXIMA 1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2018-07-06 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.97857 |
| Spacegroup name | P 41 21 2 |
| Unit cell lengths | 165.848, 165.848, 209.263 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 32.760 - 3.238 |
| R-factor | 0.2487 |
| Rwork | 0.247 |
| R-free | 0.28430 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.006 |
| RMSD bond angle | 0.790 |
| Data reduction software | XDS (Jun 30, 2023) |
| Data scaling software | Aimless (0.7.15) |
| Phasing software | PHASER (2.7) |
| Refinement software | BUSTER (2.10.4) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 129.978 | 129.978 | 3.628 |
| High resolution limit [Å] | 3.237 | 10.496 | 3.237 |
| Rmerge | 0.153 | 0.058 | 1.915 |
| Rmeas | 0.157 | 0.060 | 1.962 |
| Rpim | 0.035 | 0.014 | 0.423 |
| Total number of observations | 620053 | 26168 | 32851 |
| Number of reflections | 30990 | 1550 | 1549 |
| <I/σ(I)> | 13.06 | 37.39 | 1.9 |
| Completeness [%] | 95.7 | 100 | 77.3 |
| Completeness (spherical) [%] | 65.7 | 100.0 | 11.5 |
| Completeness (ellipsoidal) [%] | 95.7 | 100.0 | 77.3 |
| Redundancy | 20.01 | 16.88 | 21.21 |
| CC(1/2) | 0.999 | 0.999 | 0.742 |
| Anomalous completeness (spherical) | 64.3 | 100.0 | 10.6 |
| Anomalous completeness | 95.7 | 100.0 | 76.9 |
| Anomalous redundancy | 10.7 | 10.1 | 11.4 |
| CC(ano) | -0.216 | -0.319 | 0.000 |
| |DANO|/σ(DANO) | 0.7 | 0.5 | 0.7 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 3.937 Å | 1.000, 1.000, 1.000 |
| 3.937 Å | 0.000, 0.000, 0.000 |
| 3.219 Å | 0.000, 0.000, 0.000 |
| Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 294 | Well solution: 0.1 M MES pH 6.5, 0.6 M NaCl, 18% PEG4000, PLP 2 mM, Cryoprotection in glycerol 25% |
