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Crystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-1-159.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9D8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG 3350, 0.20 M Ammonium tartrate dibasic. CrpaA.01010.b.GT4.PW39259 at 16.8 mg/mL. Crystals of the WIN-3-115 inhibitor complex were soaked in 2mM WIN-1-159 in crystallant and transferred to 4 fresh drops before freezing. plate Liu-S-169 B1, Puck: PSL-1701, Cryo: 32.5% PEG 3350, 0.40 M Ammonium tartrate dibasic.
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.518 α = 90 b = 56.418 β = 104.71 c = 81.707 γ = 90
Symmetry Space Group P 1 21 1
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 2025-02-15 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 2.3 45.92 99.9 0.061 0.067 0.026 0.999 17.6 6.8 23489
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 2.31 2.37 100 0.954 1.029 0.383 0.611 7.1
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 2.3 45.92 1.36 23489 1183 99.77 0.2128 0.2111 0.2133 0.2462 0.2504
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 12.089 f_angle_d 0.764 f_chiral_restr 0.044 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3341 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing