7ZCY
Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
| Synchrotron site | PETRA III, EMBL c/o DESY |
| Beamline | P13 (MX1) |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-10-27 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9763 |
| Spacegroup name | P 63 2 2 |
| Unit cell lengths | 131.612, 131.612, 189.003 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 97.800 - 1.540 |
| R-factor | 0.13857 |
| Rwork | 0.137 |
| R-free | 0.15991 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5g4h |
| RMSD bond length | 0.013 |
| RMSD bond angle | 1.806 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | REFMAC |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 189.000 | 1.570 |
| High resolution limit [Å] | 1.540 | 1.540 |
| Rmerge | 0.094 | 2.301 |
| Rmeas | 0.099 | 2.422 |
| Rpim | 0.031 | 0.752 |
| Number of reflections | 142031 | 6976 |
| <I/σ(I)> | 20.9 | 1.6 |
| Completeness [%] | 100.0 | 100 |
| Redundancy | 19.5 | 19.9 |
| CC(1/2) | 1.000 | 0.749 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | COUNTER-DIFFUSION | 6.3 | 293 | Protein-ligand (1 mM ligand concentration) complex in 50 mM HEPES buffer, pH 7.50 (also containing 10% (V/V) DMSO), diluted 1:1 with 1.6-2.1 M ammonium sulfate also containing 100 mM sodium citrate at pH 6.3 |
