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Structure of CRBN:IKZF2:Compound 35
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.463 α = 99.92 b = 45.27 β = 90.58 c = 65.493 γ = 104.38
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 EIGER2 XE 16M 2022-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97628 Diamond I02
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 2.34 29.68 94.8 0.182 0.225 0.13 0.908 5.7 3.2 19467
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 2.34 2.42 97 0.571 0.687 0.377 0.503 3.4
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 2.34 29.68 18455 992 94.74 0.22768 0.2244 0.2297 0.28975 0.2903 RANDOM 37.426
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] 0.02 -0.01 -0.02 -0.08 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 10.99 r_long_range_B_refined 8.282 r_long_range_B_other 8.282 r_dihedral_angle_1_deg 7.823 r_mcangle_it 5.584 r_mcangle_other 5.583 r_scangle_other 4.986 r_mcbond_it 3.535 r_mcbond_other 3.534 r_scbond_it 3.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 10.99 r_long_range_B_refined 8.282 r_long_range_B_other 8.282 r_dihedral_angle_1_deg 7.823 r_mcangle_it 5.584 r_mcangle_other 5.583 r_scangle_other 4.986 r_mcbond_it 3.535 r_mcbond_other 3.534 r_scbond_it 3.199 r_scbond_other 3.199 r_angle_refined_deg 1.502 r_angle_other_deg 0.544 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4211 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction MOLREP phasing