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Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 21% PEG 3350
0.4 M KSCN
0.1 M HEPES 6.8
Crystal Properties Matthews coefficient Solvent content 2.52 51.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.702 α = 90 b = 190.809 β = 115.25 c = 48.698 γ = 90
Symmetry Space Group P 1 21 1
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 2020-12-18 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) 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 2.5 47.75 99.3 0.997 8.8 7.1 26976
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 2.5 2.6 0.786
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 2H9M 2.5 47.75 25571 1368 99.3 0.2459 0.2434 0.2475 0.2932 0.2911 RANDOM 67.574
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] -6.83 0.99 -9.07 10.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_dihedral_angle_4_deg 23.442 r_dihedral_angle_3_deg 19.629 r_dihedral_angle_1_deg 7.522 r_angle_refined_deg 1.429 r_angle_other_deg 1.183 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_dihedral_angle_4_deg 23.442 r_dihedral_angle_3_deg 19.629 r_dihedral_angle_1_deg 7.522 r_angle_refined_deg 1.429 r_angle_other_deg 1.183 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4932 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 72
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction