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Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11c
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 1.79 31.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.989 α = 90 b = 59.126 β = 90 c = 87.139 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 2022-08-19 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 1.84 37.12 100 0.999 16.62 12.9 26237
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 1.84 1.91 0.618
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.84 37.12 26213 1308 100 0.184 0.1838 0.225 0.226 43.73
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] 0.105 0.608 -0.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.042 r_dihedral_angle_2_deg 9.634 r_scangle_it 7.601 r_scangle_other 7.24 r_dihedral_angle_1_deg 6.853 r_mcangle_it 5.541 r_mcangle_other 5.539 r_scbond_it 5.365 r_scbond_other 5.01 r_mcbond_it 4.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.042 r_dihedral_angle_2_deg 9.634 r_scangle_it 7.601 r_scangle_other 7.24 r_dihedral_angle_1_deg 6.853 r_mcangle_it 5.541 r_mcangle_other 5.539 r_scbond_it 5.365 r_scbond_other 5.01 r_mcbond_it 4.108 r_mcbond_other 4.105 r_angle_refined_deg 1.352 r_angle_other_deg 0.542 r_nbd_other 0.249 r_nbd_refined 0.194 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.172 r_metal_ion_refined 0.111 r_chiral_restr 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other r_xyhbond_nbd_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1990 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing