9KWA
Crystal structure of proline dipeptidase from Pyrococcus furiosus complexed with Mn
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | RRCAT INDUS-2 BEAMLINE PX-BL21 |
| Synchrotron site | RRCAT INDUS-2 |
| Beamline | PX-BL21 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2024-10-24 |
| Detector | MARMOSAIC 225 mm CCD |
| Wavelength(s) | 0.97893 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 61.272, 71.589, 89.196 |
| Unit cell angles | 90.00, 92.84, 90.00 |
Refinement procedure
| Resolution | 46.520 - 1.850 |
| R-factor | 0.18 |
| Rwork | 0.178 |
| R-free | 0.21130 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | AlphaFold |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.018 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.21.1_5286) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 46.520 | 1.890 |
| High resolution limit [Å] | 1.850 | 1.850 |
| Rmerge | 0.086 | 1.325 |
| Rmeas | 0.092 | |
| Rpim | 0.033 | 0.515 |
| Number of reflections | 128963 | 4016 |
| <I/σ(I)> | 15 | 1.5 |
| Completeness [%] | 100.0 | 100 |
| Redundancy | 7.5 | 7.5 |
| CC(1/2) | 0.998 | 0.668 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | MICROBATCH | 8 | 294.15 | 200 mM Sodium bromide, 20% w/v PEG 3350, 20 mM Tris-Cl (pH 8.0), 200 mM NaCl (mixed in 1:1) |
