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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash II structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V2Y PDB ENTRY 4V2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100 MM TRI-SODIUM CITRATE PH 5.6, 1.0 M AMMONIUM PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 1.8 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.35 α = 90 b = 59.43 β = 90 c = 86.04 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 2012-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 37.2 97.7 0.07 9.79 2.86 30163 -3
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 1.86 96.5 0.48 2.16 2.79
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 PDB ENTRY 4V2Y 1.75 37.24 28637 1512 99.44 0.1567 0.15495 0.1659 0.19053 0.2012 RANDOM 31.362
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] -2.05 0.79 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.82 r_dihedral_angle_4_deg 12.987 r_dihedral_angle_3_deg 12.896 r_dihedral_angle_1_deg 6.437 r_scbond_it 2.609 r_angle_refined_deg 2.397 r_mcangle_it 2.179 r_mcbond_it 1.381 r_mcbond_other 1.38 r_angle_other_deg 1.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.82 r_dihedral_angle_4_deg 12.987 r_dihedral_angle_3_deg 12.896 r_dihedral_angle_1_deg 6.437 r_scbond_it 2.609 r_angle_refined_deg 2.397 r_mcangle_it 2.179 r_mcbond_it 1.381 r_mcbond_other 1.38 r_angle_other_deg 1.163 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2186 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling