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Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 0.5 M (NH4)H2PO4
Crystal Properties Matthews coefficient Solvent content 1.82 32.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.839 α = 90 b = 59.572 β = 90 c = 88.484 γ = 90
Symmetry Space Group P 21 21 21
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 S 16M 2022-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 2.3 49.42 99.97 0.997 10.48 12.9 13895
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 2.3 2.382 0.58
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 49.416 13889 693 99.993 0.207 0.2045 0.2048 0.2533 0.2544 57.484
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] -0.099 0.533 -0.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.591 r_dihedral_angle_3_deg 12.488 r_dihedral_angle_2_deg 10.631 r_dihedral_angle_1_deg 7.512 r_lrange_it 4.99 r_lrange_other 4.989 r_scangle_it 3.206 r_scangle_other 3.205 r_mcangle_it 2.317 r_mcangle_other 2.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.591 r_dihedral_angle_3_deg 12.488 r_dihedral_angle_2_deg 10.631 r_dihedral_angle_1_deg 7.512 r_lrange_it 4.99 r_lrange_other 4.989 r_scangle_it 3.206 r_scangle_other 3.205 r_mcangle_it 2.317 r_mcangle_other 2.316 r_scbond_it 1.877 r_scbond_other 1.876 r_mcbond_it 1.387 r_mcbond_other 1.386 r_angle_refined_deg 0.958 r_angle_other_deg 0.373 r_nbd_other 0.219 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.184 r_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.176 r_metal_ion_refined 0.14 r_symmetry_nbd_refined 0.131 r_ncsr_local_group_3 0.11 r_xyhbond_nbd_refined 0.108 r_ncsr_local_group_2 0.106 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.077 r_chiral_restr 0.047 r_dihedral_angle_other_2_deg 0.034 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2221 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing