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Mouse Cereblon thalidomide binding domain, native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.7 277 0.1M sodium acetate
(pH 5.7), 0.2M sodium sulphate, 12% PEG3350, 30% glycerol, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.726 α = 90 b = 117.726 β = 90 c = 117.726 γ = 90
Symmetry Space Group I 21 3
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 2011-01-26 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 18492
Refinement Statistics Diffraction ID Structure Solution 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 3WX1 2 31.46 17462 943 99.8 0.19656 0.19505 0.1956 0.2246 0.2246 RANDOM 39.001
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 44 r_dihedral_angle_3_deg 17.836 r_dihedral_angle_4_deg 17.683 r_long_range_B_refined 7.746 r_dihedral_angle_1_deg 6.265 r_scbond_it 4.664 r_mcangle_it 3.446 r_mcbond_it 2.471 r_angle_refined_deg 1.011 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44 r_dihedral_angle_3_deg 17.836 r_dihedral_angle_4_deg 17.683 r_long_range_B_refined 7.746 r_dihedral_angle_1_deg 6.265 r_scbond_it 4.664 r_mcangle_it 3.446 r_mcbond_it 2.471 r_angle_refined_deg 1.011 r_chiral_restr 0.088 r_gen_planes_refined 0.016 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 1612 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling