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Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC 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 23.5% PEG3350, 0.21 M ammonium sulfate, 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.662 α = 114.09 b = 62.276 β = 91.08 c = 64.381 γ = 110.17
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 2019-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.000 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 1.33 32.35 88.9 0.063 7.15 2.3 133465
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 1.33 1.363 1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 8F1G 1.33 32.35 126790 6674 94.86 0.14066 0.13908 0.17047 0.1856 RANDOM 20.439
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] -0.09 0.26 -0.14 0.59 0.1 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.899 r_dihedral_angle_4_deg 22.726 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 8.368 r_rigid_bond_restr 4.291 r_long_range_B_refined 3.113 r_long_range_B_other 2.733 r_scangle_other 2.076 r_scbond_it 1.727 r_mcangle_other 1.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.899 r_dihedral_angle_4_deg 22.726 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 8.368 r_rigid_bond_restr 4.291 r_long_range_B_refined 3.113 r_long_range_B_other 2.733 r_scangle_other 2.076 r_scbond_it 1.727 r_mcangle_other 1.685 r_mcangle_it 1.684 r_scbond_other 1.653 r_angle_other_deg 1.644 r_mcbond_it 1.349 r_mcbond_other 1.349 r_angle_refined_deg 1.323 r_chiral_restr 0.066 r_bond_other_d 0.018 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4765 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing