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Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma brucei (hesperidin)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9Z8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 Index A3: 0.1M Bis-Tris pH 5.5, 2.0M Ammonium Sulfate. TrbrA.01480.a.WW4.PS38793 at 13.5 mg/mL. The C-terminal tail ~60 residues was disordered in each subunit. 24h soak in 2mM hesparidin in crystallant. plate BK6-pg64Clover-C3, IDX A3, Puck: PSL-0304, Cryo: 2.5M Li2SO4. Anisotropically truncated data were used for refinement.
Crystal Properties Matthews coefficient Solvent content 2.33 47.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.16 α = 90 b = 88.94 β = 90 c = 200.26 γ = 90
Symmetry Space Group I 2 2 2
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 2026-06-13 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 2.65 81.284 79.5 0.148 0.16 0.06 0.998 13.6 13.2 18123
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 2.65 2.747 39.7 1.678 1.807 0.667 0.638 1.7 13.6
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 2.65 79.15 1.35 18116 914 79.49 0.2224 0.2199 0.2205 0.2696 0.2641
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 15.283 f_angle_d 0.785 f_chiral_restr 0.05 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4167 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 146
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction