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Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 8d
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 1.81 32.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.793 α = 90 b = 59.519 β = 90 c = 88.149 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 2021-08-27 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 1.47 49.33 99.97 0.999 15.28 12.9 51535
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 1.47 1.523 0.664 1.09
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 1.47 49.327 51535 2577 99.973 0.216 0.2147 0.2147 0.2378 0.2377 31.333
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] -0.354 0.493 -0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 19.404 r_dihedral_angle_3_deg 11.461 r_dihedral_angle_2_deg 7.227 r_dihedral_angle_1_deg 6.619 r_lrange_it 6.414 r_scangle_it 5.28 r_scbond_it 3.462 r_mcangle_it 3.089 r_mcbond_it 2.072 r_angle_refined_deg 1.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 19.404 r_dihedral_angle_3_deg 11.461 r_dihedral_angle_2_deg 7.227 r_dihedral_angle_1_deg 6.619 r_lrange_it 6.414 r_scangle_it 5.28 r_scbond_it 3.462 r_mcangle_it 3.089 r_mcbond_it 2.072 r_angle_refined_deg 1.503 r_nbtor_refined 0.319 r_symmetry_nbd_refined 0.3 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.188 r_metal_ion_refined 0.114 r_symmetry_xyhbond_nbd_refined 0.103 r_chiral_restr 0.082 r_gen_planes_refined 0.012 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2254 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing