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Crystal structure of CRBN-midi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PDB deposition D_1292135928
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M sodium citrate, 20% (w/v) PEG 3350, and 0.1 M BIS-TRIS propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.031 α = 90 b = 96.405 β = 90 c = 148.086 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 6M 2023-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.00 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3.11 74.04 100 0.41 0.98 5 11.7 6975 88.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.11 3.16 100 6.797 0.37 0.7 11.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.11 74.04 1.34 6975 359 99.5 0.2684 0.2667 0.267 0.2997 0.3019 81.15
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 f_dihedral_angle_d 12.9669 f_angle_d 0.6046 f_chiral_restr 0.0419 f_plane_restr 0.0044 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2119 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing Coot model building