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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220)
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 293 0.5 M (NH4)H2PO4
Crystal Properties Matthews coefficient Solvent content 1.78 31.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.001 α = 90 b = 58.85 β = 90 c = 88.583 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 PILATUS 6M-F 2018-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 34.76 97.7 0.135 0.141 0.998 11.24 12.5 27318
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 94.9 1.542 1.611 0.845 1.21 11
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4v2y 1.8 34.76 25945 1373 97.73 0.1956 0.1929 0.2002 0.2462 0.2441 RANDOM 37.589
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] 0.04 -0.09 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_3_deg 12.212 r_dihedral_angle_1_deg 7.58 r_angle_refined_deg 1.546 r_angle_other_deg 1.335 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_3_deg 12.212 r_dihedral_angle_1_deg 7.58 r_angle_refined_deg 1.546 r_angle_other_deg 1.335 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing