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Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 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 6.8 293 21-28% PEG 3350 0.4 M KSCN 0.1 M HEPES pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.786 α = 90 b = 184.506 β = 102.78 c = 47.951 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 PILATUS 2M-F 2022-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999998 SLS X06DA
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 2.8 184.51 100 0.105 0.149 0.105 0.984 6 2 19494
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 2.8 2.95 100 0.459 0.65 0.459 0.707 2
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 2.8 92.25 18571 888 99.99 0.2062 0.2027 0.2076 0.279 0.2765 RANDOM 48.286
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] 2.81 2.42 -2.27 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.4 r_dihedral_angle_1_deg 8.311 r_dihedral_angle_2_deg 6.423 r_angle_refined_deg 1.199 r_angle_other_deg 0.433 r_chiral_restr 0.052 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4948 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 71
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction