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Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8F8E experimental model PDB 2GNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 5% w/v 1-ethyl-3-methylimidazolium ethyl sulfate, 15% w/v polyethylene glycol 20,000, pH 7.9
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.213 α = 90 b = 85.143 β = 90 c = 111.644 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2024-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.1808 CLSI 08B1-1
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 2.06 42.57 95.17 0.01625 0.02298 0.01625 1 25.11 2 49405 37.78
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 2.06 2.1 0.6408 0.9062 0.6408 0.952 1.05
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 2.06 42.57 1.33 47891 2395 95.18 0.2117 0.2108 0.2111 0.2291 0.2287 46.56
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 13.9745 f_angle_d 1.8364 f_bond_d 0.6576 f_chiral_restr 0.0523 f_plane_restr 0.0389
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4946 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction pointless data scaling PHASER phasing