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Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form
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 64 MM SODIUM CITRATE PH 7.0, 100 MM HEPES PH 7.0, 10 %(W/V) PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 3.8 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.86 α = 90 b = 137.86 β = 90 c = 154.39 γ = 120
Symmetry Space Group P 61 2 2
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 2011-06-24 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 2.9 39 99.1 0.1 10.53 2.97 19746 -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 2.9 3.07 98.3 0.53 2.22 2.95
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 PDB ENTRY 4V2Y 2.9 38.98 18776 989 99.65 0.17664 0.17452 0.21688 0.1978 RANDOM 48.624
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] -0.65 -0.32 -0.65 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_3_deg 19.674 r_dihedral_angle_4_deg 14.071 r_dihedral_angle_1_deg 7.979 r_mcangle_it 2.846 r_scbond_it 2.144 r_angle_refined_deg 1.952 r_mcbond_it 1.759 r_mcbond_other 1.758 r_angle_other_deg 1.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_3_deg 19.674 r_dihedral_angle_4_deg 14.071 r_dihedral_angle_1_deg 7.979 r_mcangle_it 2.846 r_scbond_it 2.144 r_angle_refined_deg 1.952 r_mcbond_it 1.759 r_mcbond_other 1.758 r_angle_other_deg 1.038 r_chiral_restr 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 3308 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing