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Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Q2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 21% PEG 3350, 0.4-1 M KSCN 0.1 M HEPES pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.12 α = 90 b = 86.689 β = 90 c = 196.6 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 X 16M 2021-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999998 SLS X06SA
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 2.2 49.2 99.8 0.166 0.176 0.058 0.997 10.1 9.1 42660
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 2.2 2.27 99.8 1.012 1.072 0.345 0.83 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7Q2J 2.2 49.2 40492 2090 99.6 0.2022 0.1999 0.209 0.2479 0.2479 RANDOM 34.401
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] -3.59 6.97 -3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.321 r_dihedral_angle_1_deg 7.886 r_dihedral_angle_2_deg 6.992 r_angle_refined_deg 1.419 r_angle_other_deg 0.469 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5065 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction