☰ Navigation Tabs
PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BQV experimental model PDB 7LPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.4 M Magnesium chloride
0.1 M TRIS pH 7.5
27% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.01 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.395 α = 90 b = 69.239 β = 90.01 c = 79.857 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 95 PIXEL DECTRIS EIGER2 X 16M 2022-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.69 79.86 84.8 0.077 0.998 13.3 6.4 46939
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72 0.653 0.826 4.9
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 1.69 79.86 44747 2166 84.64 0.21164 0.21053 0.2164 0.2342 0.2418 RANDOM 22.825
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] 0.19 -0.02 -0.29 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.999 r_dihedral_angle_3_deg 14.924 r_dihedral_angle_1_deg 6.35 r_long_range_B_refined 5.4 r_long_range_B_other 5.376 r_scangle_other 3.671 r_mcangle_it 2.988 r_mcangle_other 2.988 r_scbond_it 2.385 r_scbond_other 2.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.999 r_dihedral_angle_3_deg 14.924 r_dihedral_angle_1_deg 6.35 r_long_range_B_refined 5.4 r_long_range_B_other 5.376 r_scangle_other 3.671 r_mcangle_it 2.988 r_mcangle_other 2.988 r_scbond_it 2.385 r_scbond_other 2.385 r_mcbond_it 2.015 r_mcbond_other 2.012 r_angle_refined_deg 1.901 r_angle_other_deg 0.503 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4211 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing