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Crystal Structure of Cdk-related protein kinase 6 (PK6) from Plasmodium falciparum in complex with inhibitor KG2-051
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8U2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Berkeley F7: 20% (w/v) PEG MME 5000, 100 mM Tris pH 8.5, 200 mM lithium sulfate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM KG2-051 added prior to crystallization. plate SS CloverBook4_pg5, Cryo: 80% crystallant + 20% PEG200.
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.539 α = 90 b = 99.428 β = 100.78 c = 78.148 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 Bruker PHOTON III 2024-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
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 2.45 44.4 99.3 0.122 0.127 0.037 0.987 18.8 11.6 42580
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 2.45 2.54 99.6 1.894 1.99 0.602 0.698 10.3
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 2.45 34.66 1.34 42504 2094 99.03 0.2214 0.2196 0.2229 0.2553 0.258
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 19.282 f_angle_d 0.973 f_chiral_restr 0.053 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6682 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 118
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing