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Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)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 20 % PEG 3350, 0.2 M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.94 36.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.728 α = 90 b = 59.163 β = 105.59 c = 61.751 γ = 90
Symmetry Space Group P 1 21 1
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 2017-09-25 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 1.5 49.17 99 0.08 0.998 9.7 3.37 68423
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 1.5 1.59 97.5 0.88 0.56 1.15 3.14
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 1.5 49.17 65001 3422 99.64 0.15943 0.1578 0.19039 0.1652 RANDOM 21.669
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] -0.24 0.18 0.32 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.608 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 12.426 r_long_range_B_refined 7.246 r_long_range_B_other 7.229 r_dihedral_angle_1_deg 7.117 r_scangle_other 5.264 r_angle_refined_deg 4.409 r_mcangle_it 3.844 r_mcangle_other 3.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.608 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 12.426 r_long_range_B_refined 7.246 r_long_range_B_other 7.229 r_dihedral_angle_1_deg 7.117 r_scangle_other 5.264 r_angle_refined_deg 4.409 r_mcangle_it 3.844 r_mcangle_other 3.844 r_scbond_it 3.407 r_scbond_other 3.406 r_mcbond_it 2.641 r_mcbond_other 2.635 r_angle_other_deg 1.407 r_chiral_restr 0.198 r_gen_planes_refined 0.043 r_bond_refined_d 0.037 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 3425 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing