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Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11a
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 1.8 31.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.511 α = 90 b = 59.542 β = 90 c = 88.185 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 2.25 47.58 99.84 0.998 10.68 12.9 14648
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 2.25 2.331 0.631
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 2.25 47.58 14646 731 99.857 0.224 0.2218 0.222 0.2685 0.2693 53.339
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] -0.241 0.147 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.06 r_dihedral_angle_3_deg 10.903 r_dihedral_angle_2_deg 6.687 r_dihedral_angle_1_deg 6.003 r_lrange_it 3.768 r_lrange_other 3.767 r_scangle_it 2.297 r_scangle_other 2.296 r_mcangle_it 1.826 r_mcangle_other 1.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.06 r_dihedral_angle_3_deg 10.903 r_dihedral_angle_2_deg 6.687 r_dihedral_angle_1_deg 6.003 r_lrange_it 3.768 r_lrange_other 3.767 r_scangle_it 2.297 r_scangle_other 2.296 r_mcangle_it 1.826 r_mcangle_other 1.826 r_scbond_it 1.379 r_scbond_other 1.379 r_mcbond_it 1.068 r_mcbond_other 1.068 r_angle_refined_deg 0.758 r_angle_other_deg 0.309 r_nbd_other 0.221 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.179 r_metal_ion_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.165 r_nbd_refined 0.159 r_symmetry_nbd_refined 0.146 r_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.078 r_ncsr_local_group_3 0.074 r_ncsr_local_group_2 0.067 r_chiral_restr 0.038 r_dihedral_angle_other_2_deg 0.028 r_symmetry_xyhbond_nbd_other 0.01 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2185 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing