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Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 IDX G2 (25% (w/v) PEG 3350, 0.1 M BIS-TRIS pH 5.5, 0.2 M lithium sulfate. TrbrA.01480.a.WW4.PS38793 at 13.5 mg/mL. The C-terminal tail ~60 residues was disordered in each subunit. Residue Ser 71 in subunit A contained a large amount of density near the OG atom. This was modeled as a phosphoserine (SEP) although this is not a predicted phosphorylation site. plate 20520 G2 drop 1, Puck: PSL-0604, Cryo: 80% crystallant + 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.599 α = 90 b = 89.098 β = 90 c = 201.567 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 2025-11-01 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 2.05 43.3 100 0.088 0.092 0.025 0.999 16.4 13.3 49269
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 2.05 2.11 99.9 1.617 1.678 0.447 0.815 13.9
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 2.05 43.3 1.33 49253 2552 99.92 0.1966 0.1946 0.1988 0.2348 0.2373
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 16.494 f_angle_d 0.644 f_chiral_restr 0.046 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4374 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MoRDa phasing PDB_EXTRACT data extraction