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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aminoglutarimide degron peptide
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 294 0.5 M (NH4)H2PO4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.606 α = 90 b = 59.45 β = 90 c = 89.059 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 2022-09-23 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 1.719 49.446 100 0.104 0.999 12.2 13.05 32675
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 1.72 1.82 100 1.91 0.632 1.18 13.54
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 1.719 49.446 32675 1633 99.957 0.176 0.1743 0.1851 0.2111 0.2185 41.172
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] -0.695 1.396 -0.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.414 r_dihedral_angle_4_deg 17.528 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_1_deg 7.055 r_lrange_it 6.249 r_lrange_other 6.24 r_scangle_it 4.34 r_scangle_other 4.339 r_scbond_it 2.784 r_scbond_other 2.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.414 r_dihedral_angle_4_deg 17.528 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_1_deg 7.055 r_lrange_it 6.249 r_lrange_other 6.24 r_scangle_it 4.34 r_scangle_other 4.339 r_scbond_it 2.784 r_scbond_other 2.782 r_mcangle_it 2.623 r_mcangle_other 2.623 r_mcbond_it 1.789 r_mcbond_other 1.785 r_angle_refined_deg 1.76 r_angle_other_deg 1.458 r_symmetry_xyhbond_nbd_refined 0.387 r_nbd_refined 0.213 r_symmetry_nbd_other 0.204 r_xyhbond_nbd_refined 0.191 r_nbd_other 0.19 r_nbtor_refined 0.181 r_ncsr_local_group_3 0.143 r_ncsr_local_group_2 0.141 r_ncsr_local_group_1 0.125 r_chiral_restr 0.103 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2426 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling