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Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41114
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 6.9 294 1.8 M Sodium phosphate monobasic monohydrate, potassium phosphate dibasic / pH 6.9
Crystal Properties Matthews coefficient Solvent content 2.96 58.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.225 α = 90 b = 83.882 β = 90 c = 131.483 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 EIGER R 1M 2024-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002+ 1.54189
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 2.07 28.59 95.8 0.989 7.69 4.4 52605 17.3
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 2.07 2.11 0.448
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 2.07 28.59 1.33 52465 2645 95.8 0.2018 0.1997 0.198 0.2422 0.24 20.66
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 14.3802 f_angle_d 0.9556 f_chiral_restr 0.0563 f_bond_d 0.0113 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4833 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling PHENIX phasing