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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash I 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 SODIUM ACETATE PH 4.6, 20 %(W/V) PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.8 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.25 α = 90 b = 59.656 β = 90 c = 86.728 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 2013-12-13 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 37.3 99.7 0.05 16.98 4.23 30628 -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 98.7 0.68 1.9 4.23
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 37.29 29087 1540 99.75 0.16727 0.16508 0.1761 0.20942 0.219 RANDOM 36.758
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] 1.1 0.03 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_3_deg 13.114 r_dihedral_angle_4_deg 12.405 r_dihedral_angle_1_deg 6.22 r_mcangle_it 2.566 r_scbond_it 2.525 r_angle_refined_deg 2.235 r_mcbond_it 1.665 r_mcbond_other 1.664 r_angle_other_deg 1.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_3_deg 13.114 r_dihedral_angle_4_deg 12.405 r_dihedral_angle_1_deg 6.22 r_mcangle_it 2.566 r_scbond_it 2.525 r_angle_refined_deg 2.235 r_mcbond_it 1.665 r_mcbond_other 1.664 r_angle_other_deg 1.155 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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 2232 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling