8DL5
Crystal structure of PLP-dependent Mannich cyclase LolT
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL9-2 |
Synchrotron site | SSRL |
Beamline | BL9-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-12-05 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97946 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 77.837, 77.837, 298.842 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 37.660 - 2.100 |
R-factor | 0.2344 |
Rwork | 0.233 |
R-free | 0.26080 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | Alphafold2 predicted model |
RMSD bond length | 0.004 |
RMSD bond angle | 0.866 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | PHASER |
Refinement software | PHENIX (1.18.2_3874) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.150 |
High resolution limit [Å] | 2.100 | 2.110 |
Rpim | 0.042 | 0.600 |
Number of reflections | 62480 | 3034 |
<I/σ(I)> | 27.22 | 1.7 |
Completeness [%] | 100.0 | 100 |
Redundancy | 18.8 | 16.7 |
CC(1/2) | 0.974 | 0.713 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 292 | 0.1 M sodium malonate, pH 5.18, 14% w/v PEG3350 |