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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5b
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 0.4 M Ammonium Phosphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.66 α = 90 b = 58.709 β = 90 c = 88.013 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 2018-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 47.64 99.6 0.066 20.47 12.76 30381
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 97.7 0.99 2.27 12.8
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 1.75 47.64 28865 1516 99.6 0.19 0.188 0.2018 0.227 0.2341 RANDOM 41.47
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] -1.06 1.72 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_4_deg 9.199 r_dihedral_angle_1_deg 6.442 r_long_range_B_refined 5.902 r_long_range_B_other 5.858 r_scangle_other 3.329 r_mcangle_it 2.704 r_mcangle_other 2.703 r_scbond_it 2.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_4_deg 9.199 r_dihedral_angle_1_deg 6.442 r_long_range_B_refined 5.902 r_long_range_B_other 5.858 r_scangle_other 3.329 r_mcangle_it 2.704 r_mcangle_other 2.703 r_scbond_it 2.082 r_scbond_other 2.081 r_mcbond_it 1.783 r_mcbond_other 1.774 r_angle_refined_deg 1.726 r_angle_other_deg 1.023 r_chiral_restr 0.119 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2485 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing