☰ Navigation Tabs
Crystal Structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum (AMP/Mg bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 25% (w/v) PEG3350, 0.2M diammonium tartrate. CrpaA.01010.b.GT4.PW39259 at 15 mg/mL. Cocrystallized with 5mM AMP, 4mM MgCl2 and 2mM CaCl2. Plate: Liu-S-131 A10, Puck: PSL-1109, Cryo: 20% (v/v) PEG 200 + 80% (w/v) crystallant
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.746 α = 90 b = 55.746 β = 105.64 c = 81.954 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 2024-08-03 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 2.12 78.92 99.9 0.082 0.092 0.041 0.998 9.9 4.9 29675
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 2.12 2.18 100 0.989 1.107 0.491 0.633 4.9
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 2.12 57.53 1.35 29638 1450 99.76 0.2103 0.2086 0.2122 0.2433 0.2395
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 12.159 f_angle_d 0.789 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3265 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing