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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8a
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 3mM thalidomide
Crystal Properties Matthews coefficient Solvent content 1.8 31.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.356 α = 90 b = 59.597 β = 90 c = 87.875 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 2023-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0001 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.76 47.48 100 0.13 0.997 8.06 6.89 56873 38.389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 99.8 0.13 0.562 1.04 6.4
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 1.76 47.48 28622 1506 99.95 0.18771 0.18551 0.1934 0.23045 0.2332 RANDOM 35.359
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] -2.01 3.35 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.032 r_dihedral_angle_4_deg 14.652 r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 7.293 r_long_range_B_refined 5.249 r_long_range_B_other 5.203 r_scangle_other 2.877 r_mcangle_it 2.12 r_mcangle_other 2.12 r_scbond_it 1.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.032 r_dihedral_angle_4_deg 14.652 r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 7.293 r_long_range_B_refined 5.249 r_long_range_B_other 5.203 r_scangle_other 2.877 r_mcangle_it 2.12 r_mcangle_other 2.12 r_scbond_it 1.851 r_scbond_other 1.798 r_angle_refined_deg 1.728 r_angle_other_deg 1.421 r_mcbond_it 1.326 r_mcbond_other 1.326 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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 2384 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building