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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2n
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, HANGING DROP 293 0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide
Crystal Properties Matthews coefficient Solvent content 1.82 32.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.609 α = 90 b = 59.756 β = 90 c = 88.464 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 2024-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.49 50 99.6 0.999 12.32 12.88 49304 27.73
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 1.49 1.58 97.8 0.638 1.29 12.44
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.49 41.13 46839 2465 99.61 0.17763 0.17596 0.1763 0.21003 0.2098 RANDOM 25.212
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] 0.1 0.62 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.093 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 12.314 r_dihedral_angle_1_deg 6.792 r_long_range_B_refined 4.507 r_long_range_B_other 4.485 r_scangle_other 2.475 r_angle_refined_deg 1.707 r_mcangle_it 1.702 r_mcangle_other 1.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.093 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 12.314 r_dihedral_angle_1_deg 6.792 r_long_range_B_refined 4.507 r_long_range_B_other 4.485 r_scangle_other 2.475 r_angle_refined_deg 1.707 r_mcangle_it 1.702 r_mcangle_other 1.701 r_scbond_it 1.604 r_scbond_other 1.603 r_angle_other_deg 1.497 r_mcbond_it 1.048 r_mcbond_other 1.048 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2426 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building