9GJ9
Crystal structure of methionine gamma-lyase from Brevibacterium sandarakinum in complex with PLP and norleucine at pH 6.5
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 | 2022-04-22 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.978565 |
| Spacegroup name | C 2 2 21 |
| Unit cell lengths | 132.574, 229.734, 155.174 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 114.867 - 2.492 |
| R-factor | 0.2568 |
| Rwork | 0.255 |
| R-free | 0.28700 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.005 |
| RMSD bond angle | 0.720 |
| Data reduction software | autoPROC |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.10.4) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 114.867 | 114.867 | 2.862 |
| High resolution limit [Å] | 2.492 | 8.470 | 2.492 |
| Rmerge | 0.325 | 0.098 | 0.780 |
| Rmeas | 0.352 | 0.106 | 0.887 |
| Rpim | 0.132 | 0.039 | 0.411 |
| Total number of observations | 228757 | 15445 | 7138 |
| Number of reflections | 34324 | 2268 | 1651 |
| <I/σ(I)> | 4.27 | 9.67 | 1.56 |
| Completeness [%] | 89.3 | 99.2 | 65.2 |
| Completeness (spherical) [%] | 41.5 | 99.2 | 5.9 |
| Completeness (ellipsoidal) [%] | 89.3 | 99.2 | 65.2 |
| Redundancy | 6.66 | 6.81 | 4.32 |
| CC(1/2) | 0.983 | 0.994 | 0.707 |
| Anomalous completeness (spherical) | 40.3 | 99.4 | 5.3 |
| Anomalous completeness | 88.8 | 99.4 | 62.6 |
| Anomalous redundancy | 3.5 | 3.8 | 2.3 |
| CC(ano) | -0.004 | -0.077 | -0.009 |
| |DANO|/σ(DANO) | 0.6 | 0.6 | 0.6 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 2.492 Å | 1.000, 1.000, 1.000 |
| 2.902 Å | 0.000, 0.000, 0.000 |
| 4.693 Å | 0.000, 0.000, 0.000 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | Modified Morpheus I condition 2-4: 0.1 M Ethylene glycols, 0.08 M MES/Imidazole pH 6.5, 30% MPD, 10% PEG 1000, 10% PEG3350 and 5 mM Norleucine with 1 mM PLP Protein in starting drop: 7.4 mg ml-1 in 50 mM HEPES, pH 7.5, 100 mM NaCl, 0.5 mM TCEP, 1 mM PLP |
