9PFY
Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with ATP
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS-II BEAMLINE 19-ID |
| Synchrotron site | NSLS-II |
| Beamline | 19-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2025-05-25 |
| Detector | DECTRIS EIGER2 XE 9M |
| Wavelength(s) | 0.9786 |
| Spacegroup name | P 65 2 2 |
| Unit cell lengths | 69.815, 69.815, 315.861 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 48.010 - 1.420 |
| R-factor | 0.1284 |
| Rwork | 0.127 |
| R-free | 0.15580 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.015 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX ((dev_5438: ???)) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 48.010 | 1.460 |
| High resolution limit [Å] | 1.420 | 1.420 |
| Rmerge | 0.071 | 0.618 |
| Rmeas | 0.073 | 0.700 |
| Rpim | 0.017 | 0.318 |
| Total number of observations | 1338263 | 26438 |
| Number of reflections | 86973 | 5944 |
| <I/σ(I)> | 23.3 | 1.8 |
| Completeness [%] | 99.5 | |
| Redundancy | 15.4 | 4.4 |
| CC(1/2) | 1.000 | 0.720 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 291 | Berkeley F12: 35% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystal was transferred to 35% MPD, 100mM Bis-Tris, pH 5.5, 100mM sodium formate two times and then soaked with in the same solution containing 10mM ATP for 3 hours. Subunits A and C have partial occupancy of ATP and HIP in the active site. Subunit B had 100% conversion to HIP. plate Liu-S-177 D2, Puck: PSL-0105, Cryo: direct from soaking solution |
