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Mouse Cereblon thalidomide binding domain complexed with R-form 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 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.615 α = 90 b = 201.615 β = 90 c = 123.572 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 MX-225 2011-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 50 99.9 0.078 20.6 5.8 130317
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 1.98 2.05 99.9 0.493 3.9 5.6
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 19.78 120034 6364 99.89 0.20025 0.19882 0.1987 0.22766 0.2278 RANDOM 32.721
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] 0.01 0.01 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.227 r_dihedral_angle_4_deg 22.617 r_dihedral_angle_3_deg 17.38 r_dihedral_angle_1_deg 8.019 r_long_range_B_refined 6.993 r_scbond_it 4.003 r_mcangle_it 3.377 r_mcbond_it 2.363 r_angle_refined_deg 1.258 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.227 r_dihedral_angle_4_deg 22.617 r_dihedral_angle_3_deg 17.38 r_dihedral_angle_1_deg 8.019 r_long_range_B_refined 6.993 r_scbond_it 4.003 r_mcangle_it 3.377 r_mcbond_it 2.363 r_angle_refined_deg 1.258 r_chiral_restr 0.08 r_gen_planes_refined 0.02 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 11798 Nucleic Acid Atoms Solvent Atoms 786 Heterogen Atoms 470
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing