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Mouse Cereblon thalidomide binding domain complexed with racemic thalidomide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1.0M ammonium sulfate
0.1M sodium acetate (pH5.0)
Crystal Properties Matthews coefficient Solvent content 2.44 49.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.376 α = 90 b = 201.376 β = 90 c = 123.358 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2011-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 100 20.6 5.8 125695
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 3WX2 2 38.06 119353 6311 99.9 0.18541 0.18398 0.1891 0.21252 0.22 RANDOM 29.197
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.925 r_dihedral_angle_4_deg 25.533 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_1_deg 7.893 r_long_range_B_refined 7.714 r_long_range_B_other 7.528 r_scangle_other 5.65 r_scbond_it 4.208 r_scbond_other 4.178 r_mcangle_other 3.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.925 r_dihedral_angle_4_deg 25.533 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_1_deg 7.893 r_long_range_B_refined 7.714 r_long_range_B_other 7.528 r_scangle_other 5.65 r_scbond_it 4.208 r_scbond_other 4.178 r_mcangle_other 3.757 r_mcangle_it 3.752 r_angle_other_deg 3.493 r_mcbond_other 2.62 r_mcbond_it 2.619 r_angle_refined_deg 0.961 r_chiral_restr 0.076 r_gen_planes_other 0.037 r_gen_planes_refined 0.018 r_bond_refined_d 0.005 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11838 Nucleic Acid Atoms Solvent Atoms 980 Heterogen Atoms 470
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing