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Crystal structure of the human WDR5 in complex with LH168 compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG3350, 0.2 M Ammonium formate
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.951 α = 110.41 b = 61.185 β = 91.22 c = 64.605 γ = 112.2
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 PILATUS3 S 6M 2024-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18049 CLSI 08B1-1
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 1.7 50 94.1 0.046 0.055 0.029 0.994 8.3 3.4 63599
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 1.7 1.73 80.6 0.316 0.376 0.2 0.936 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 42.89 62385 1212 93.93 0.14033 0.1394 0.1506 0.18872 0.19 RANDOM 22.816
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] 0.06 -0.25 -0.91 1.88 0.31 -1.67
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.649 r_dihedral_angle_3_deg 11.541 r_long_range_B_other 11.381 r_dihedral_angle_1_deg 8.353 r_scangle_other 6.921 r_mcangle_it 6.527 r_mcangle_other 6.527 r_dihedral_angle_2_deg 5.241 r_scbond_it 4.589 r_scbond_other 4.589
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.649 r_dihedral_angle_3_deg 11.541 r_long_range_B_other 11.381 r_dihedral_angle_1_deg 8.353 r_scangle_other 6.921 r_mcangle_it 6.527 r_mcangle_other 6.527 r_dihedral_angle_2_deg 5.241 r_scbond_it 4.589 r_scbond_other 4.589 r_mcbond_it 4.28 r_mcbond_other 4.272 r_rigid_bond_restr 2.24 r_angle_refined_deg 1.305 r_angle_other_deg 0.475 r_chiral_restr 0.065 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4711 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing