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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidine-2,6-dione (Glutarimide)
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 0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
Crystal Properties Matthews coefficient Solvent content 1.8 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.18 α = 90 b = 59.661 β = 90 c = 88.289 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 2011-09-09 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) 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 2.3 37.1 97 0.08 1 8.64 2.55 13628
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 2.3 2.44 94 0.37 0.86 1.98 2.52
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4V2Y 2.3 37.1 12940 678 98.75 0.19228 0.18929 0.25008 0.2356 RANDOM 42.714
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] -0.72 3.54 -2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 16.806 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 4.751 r_long_range_B_other 4.74 r_scangle_other 2.788 r_mcangle_it 2.019 r_mcangle_other 2.018 r_scbond_it 1.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 16.806 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 4.751 r_long_range_B_other 4.74 r_scangle_other 2.788 r_mcangle_it 2.019 r_mcangle_other 2.018 r_scbond_it 1.736 r_scbond_other 1.736 r_angle_refined_deg 1.463 r_angle_other_deg 1.315 r_mcbond_other 1.296 r_mcbond_it 1.295 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.007 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 2415 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling