☰ Navigation Tabs
Mouse Cereblon thalidomide binding domain complexed with S-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 2.46 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.897 α = 90 b = 201.897 β = 90 c = 123.614 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 2011-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.28268 SPring-8 BL41XU
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 1.8 50 100 0.081 17.8 5.6 173436
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 1.8 1.86 100 0.5 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 1.8 38.15 164742 8682 99.94 0.18972 0.18894 0.1982 0.20425 0.2129 RANDOM 29.751
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 40.439 r_dihedral_angle_4_deg 25.834 r_dihedral_angle_3_deg 16.182 r_long_range_B_refined 8.229 r_long_range_B_other 8.061 r_dihedral_angle_1_deg 7.842 r_scangle_other 6.406 r_scbond_it 4.665 r_scbond_other 4.626 r_mcangle_other 4.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.439 r_dihedral_angle_4_deg 25.834 r_dihedral_angle_3_deg 16.182 r_long_range_B_refined 8.229 r_long_range_B_other 8.061 r_dihedral_angle_1_deg 7.842 r_scangle_other 6.406 r_scbond_it 4.665 r_scbond_other 4.626 r_mcangle_other 4.435 r_mcangle_it 4.428 r_angle_other_deg 3.476 r_mcbond_it 3.302 r_mcbond_other 3.301 r_angle_refined_deg 0.665 r_chiral_restr 0.047 r_gen_planes_other 0.032 r_gen_planes_refined 0.018 r_bond_refined_d 0.002 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 992 Heterogen Atoms 470
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing