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9PFY

Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with ATP

Experimental procedure
Experimental methodSINGLE WAVELENGTH
Source typeSYNCHROTRON
Source detailsNSLS-II BEAMLINE 19-ID
Synchrotron siteNSLS-II
Beamline19-ID
Temperature [K]100
Detector technologyPIXEL
Collection date2025-05-25
DetectorDECTRIS EIGER2 XE 9M
Wavelength(s)0.9786
Spacegroup nameP 65 2 2
Unit cell lengths69.815, 69.815, 315.861
Unit cell angles90.00, 90.00, 120.00
Refinement procedure
Resolution48.010 - 1.420
R-factor0.1284
Rwork0.127
R-free0.15580
Structure solution methodMOLECULAR REPLACEMENT
RMSD bond length0.007
RMSD bond angle1.015
Data reduction softwareXDS
Data scaling softwareAimless
Phasing softwarePHASER
Refinement softwarePHENIX ((dev_5438: ???))
Data quality characteristics
 OverallOuter shell
Low resolution limit [Å]48.0101.460
High resolution limit [Å]1.4201.420
Rmerge0.0710.618
Rmeas0.0730.700
Rpim0.0170.318
Total number of observations133826326438
Number of reflections869735944
<I/σ(I)>23.31.8
Completeness [%]99.5
Redundancy15.44.4
CC(1/2)1.0000.720
Crystallization Conditions
crystal IDmethodpHtemperaturedetails
1VAPOR DIFFUSION, SITTING DROP5.5291Berkeley 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

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PDB entries from 2025-07-23

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