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Cereblon in complex with DDB1, GSPT1 and Compound-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.03 69.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.34 α = 90 b = 112.38 β = 95.25 c = 177.94 γ = 90
Symmetry Space Group P 1 2 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 EIGER X 16M 2024-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.9 49.49 96.5 0.978 5.06 4.44 55075
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.14 96.8 0.483 1.11
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.9 49.49 52973 2100 96.5 0.26245 0.25949 0.33557 0.2964 RANDOM 134.396
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] 6.97 2.29 -6.65 -0.72
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.873 r_long_range_B_other 24.873 r_dihedral_angle_3_deg 18.078 r_mcangle_it 17.481 r_mcangle_other 17.48 r_scangle_other 15.842 r_mcbond_it 10.367 r_mcbond_other 10.367 r_dihedral_angle_1_deg 9.412 r_scbond_it 8.828
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.873 r_long_range_B_other 24.873 r_dihedral_angle_3_deg 18.078 r_mcangle_it 17.481 r_mcangle_other 17.48 r_scangle_other 15.842 r_mcbond_it 10.367 r_mcbond_other 10.367 r_dihedral_angle_1_deg 9.412 r_scbond_it 8.828 r_scbond_other 8.827 r_dihedral_angle_2_deg 7.385 r_angle_refined_deg 1.326 r_angle_other_deg 0.471 r_chiral_restr 0.062 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25975 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing