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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a
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, SITTING DROP 294 0.4M Ammonium Phosphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.66 α = 90 b = 59.169 β = 90 c = 88.334 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 X 16M 2021-07-10 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) R Merge I (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 2.088 49.2 100 0.064 0.999 17.04 7 18215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.21 99.9 0.857 0.784 2 6.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS FREE R-VALUE 4v2y 2.088 49.16 18215 905 99.929 0.196 0.1945 0.2009 0.2325 0.2371 49.942
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] 0.767 0.492 -1.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.906 r_dihedral_angle_3_deg 12.829 r_dihedral_angle_4_deg 10.232 r_dihedral_angle_1_deg 7.181 r_lrange_it 4.333 r_lrange_other 4.332 r_scangle_it 3.116 r_scangle_other 3.115 r_mcangle_it 2.388 r_mcangle_other 2.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.906 r_dihedral_angle_3_deg 12.829 r_dihedral_angle_4_deg 10.232 r_dihedral_angle_1_deg 7.181 r_lrange_it 4.333 r_lrange_other 4.332 r_scangle_it 3.116 r_scangle_other 3.115 r_mcangle_it 2.388 r_mcangle_other 2.387 r_scbond_it 1.95 r_scbond_other 1.949 r_mcbond_other 1.539 r_mcbond_it 1.538 r_angle_refined_deg 1.463 r_angle_other_deg 1.263 r_nbd_other 0.211 r_symmetry_nbd_other 0.189 r_nbd_refined 0.172 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.166 r_xyhbond_nbd_refined 0.135 r_symmetry_nbd_refined 0.131 r_ncsr_local_group_1 0.11 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1885 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling