9JFN
Arginine decarboxylase in Aspergillus oryzae complexed with agmatine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL26B1 |
Synchrotron site | SPring-8 |
Beamline | BL26B1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2024-05-12 |
Detector | DECTRIS EIGER R 4M |
Wavelength(s) | 1.000 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 133.749, 197.286, 196.412 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 43.490 - 2.150 |
R-factor | 0.1777 |
Rwork | 0.176 |
R-free | 0.21350 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | AlphaFold |
RMSD bond length | 0.006 |
RMSD bond angle | 0.795 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHENIX |
Refinement software | PHENIX (1.21.1_5286) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.280 |
High resolution limit [Å] | 2.150 | 2.150 |
Rmerge | 0.009 | 0.968 |
Rmeas | 0.010 | 1.022 |
Number of reflections | 140013 | 22183 |
<I/σ(I)> | 17.86 | 2.47 |
Completeness [%] | 99.7 | 98.6 |
Redundancy | 9.19 | 9.53 |
CC(1/2) | 0.999 | 0.884 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 0.1 M sodium acetate buffer (pH 7.0), 12% w/v PEG 3350 The crystal was soaked in the reservoir solution with 10 mM L-agmatine for 10 min. followed by brief soaking to the same solution containing 30% ethylene glycol before flash-cooling. |