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Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum (Apo, hexamer)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9O9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Berkeley H10: 100 mM Bis-Tris pH 6.5; 200 mM Sodium acetate, 25% PEG 4000. CrpaA.01302.a.B2.PW39348 at 18.8 mg/mL. Screened as ButhA.01370.b.B2 but contaminating CrpaA.01302.a.B2 on the column from a preceding purification is what crystallized. plate 20365 H10 drop 2, Puck: PSL-1602, Cryo: 20% ethylene + 80% crystallant
Crystal Properties Matthews coefficient Solvent content 2.29 46.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.963 α = 90 b = 70.646 β = 90 c = 197.623 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 9M 2025-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.48 48.21 100 0.17 0.177 0.048 0.999 13.2 13.5 163681
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.52 100 1.768 1.835 0.489 0.672 13.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.48 48.21 1.34 163558 8297 99.98 0.13 0.1283 0.1413 0.161 0.1694
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.854 f_angle_d 0.908 f_chiral_restr 0.072 f_plane_restr 0.009 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7078 Nucleic Acid Atoms Solvent Atoms 1047 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction