☰ Navigation Tabs
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal 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 1 100 MM SODIUM ACETATE PH 4.6, 2.2 M CALCIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.3 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.72 α = 90 b = 51.72 β = 90 c = 84.71 γ = 120
Symmetry Space Group P 32 2 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 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 1.2 30.8 99.7 0.06 11.85 3.91 41611 -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 1.2 1.27 99.3 0.74 1.78 3.69
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 1.2 30.77 39531 2076 99.82 0.12716 0.12565 0.1359 0.15737 0.1661 RANDOM 24.966
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] 0.29 0.15 0.29 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.583 r_sphericity_free 30.891 r_sphericity_bonded 19.896 r_dihedral_angle_4_deg 14.455 r_dihedral_angle_3_deg 12.964 r_scbond_it 7.159 r_dihedral_angle_1_deg 6.723 r_rigid_bond_restr 6.304 r_mcangle_it 4.943 r_mcbond_it 4.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.583 r_sphericity_free 30.891 r_sphericity_bonded 19.896 r_dihedral_angle_4_deg 14.455 r_dihedral_angle_3_deg 12.964 r_scbond_it 7.159 r_dihedral_angle_1_deg 6.723 r_rigid_bond_restr 6.304 r_mcangle_it 4.943 r_mcbond_it 4.802 r_mcbond_other 4.774 r_angle_refined_deg 2.398 r_angle_other_deg 1.96 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.014 r_gen_planes_other 0.01 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 827 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing