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Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FQD in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.599 α = 90 b = 143.599 β = 90 c = 367.636 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER X 9M 2022-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95375 CLSI 08ID-1
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 3.4 56.58 98.2 0.336 0.998 12.3 38.2 31052
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.51 0.404
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 3.4 55.45 1.35 31051 1528 97.75 0.2136 0.2108 0.2106 0.2708 0.27 129.48
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 16.3221 f_angle_d 1.3295 f_chiral_restr 0.0907 f_bond_d 0.011 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12071 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement DIALS data reduction STARANISO data scaling PHASER phasing