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Crystal structure of human WDR5 in complex with N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide (compound 1, WDR5-MYC PPI inhibitor)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8F1G PDB entry 8F1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20% PEG3350, 0.2 M potassium acetate
Crystal Properties Matthews coefficient Solvent content 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.815 α = 90 b = 56.203 β = 90 c = 118.429 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 CCD ADSC QUANTUM 315r 2018-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97919 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 98.8 0.157 11.9 12.8 30595
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 1.003
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 PDB entry 8F1G 1.8 40.76 29048 1469 98.48 0.20511 0.20415 0.2103 0.22407 0.2285 RANDOM 23.761
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] -0.55 0.56 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.239 r_dihedral_angle_3_deg 13.505 r_dihedral_angle_4_deg 8.747 r_dihedral_angle_1_deg 7.057 r_long_range_B_refined 3.857 r_long_range_B_other 3.779 r_scangle_other 2.424 r_mcangle_it 1.682 r_mcangle_other 1.682 r_scbond_it 1.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.239 r_dihedral_angle_3_deg 13.505 r_dihedral_angle_4_deg 8.747 r_dihedral_angle_1_deg 7.057 r_long_range_B_refined 3.857 r_long_range_B_other 3.779 r_scangle_other 2.424 r_mcangle_it 1.682 r_mcangle_other 1.682 r_scbond_it 1.493 r_scbond_other 1.492 r_angle_refined_deg 1.199 r_mcbond_it 1.048 r_mcbond_other 1.047 r_angle_other_deg 0.686 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing