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Crystal structure of the human CDKL5 kinase domain with compound CAF-382
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BGQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.9 M lithium sulfate, 0.1 M tri-sodium citrate, and 0.7 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.37 48.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.077 α = 90 b = 89.077 β = 90 c = 132.647 γ = 120
Symmetry Space Group P 63 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 X 16M 2022-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 50.29 100 0.999 11 38.7 10172 58.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 0.839
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 2.6 50.29 1.34 10117 522 99.66 0.2282 0.226 0.2251 0.27 0.2678 65.89
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 8.7415 f_angle_d 1.8012 f_chiral_restr 0.102 f_plane_restr 0.0181 f_bond_d 0.0132
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing