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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 14r
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 0.4M Ammonium Phosphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.79 α = 90 b = 59.194 β = 90 c = 87.861 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 X 16M 2021-07-10 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 1.94 47.7 100 0.048 1 19.51 6.93 22417
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 1.94 2.06 99.9 0.979 0.733 1.7 6.99
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 1.944 47.7 22417 1119 99.947 0.198 0.1967 0.2054 0.2272 0.2324 52.323
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] 0.283 1.195 -1.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_3_deg 11.744 r_dihedral_angle_4_deg 10.777 r_dihedral_angle_1_deg 6.677 r_lrange_it 4.398 r_lrange_other 4.397 r_scangle_it 2.918 r_scangle_other 2.917 r_mcangle_it 2.195 r_mcangle_other 2.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_3_deg 11.744 r_dihedral_angle_4_deg 10.777 r_dihedral_angle_1_deg 6.677 r_lrange_it 4.398 r_lrange_other 4.397 r_scangle_it 2.918 r_scangle_other 2.917 r_mcangle_it 2.195 r_mcangle_other 2.194 r_scbond_it 1.845 r_scbond_other 1.845 r_angle_refined_deg 1.496 r_mcbond_other 1.413 r_mcbond_it 1.412 r_angle_other_deg 1.232 r_nbd_other 0.221 r_symmetry_nbd_other 0.183 r_nbd_refined 0.175 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.142 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.139 r_ncsr_local_group_1 0.109 r_symmetry_xyhbond_nbd_other 0.103 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2017 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling