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Keap1 kelch domain bound to a small molecule inhibitor of the Keap1-Nrf2 protein-protein interaction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6 and 1.0 M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.19 α = 90 b = 103.19 β = 90 c = 55.6 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 PIXEL DECTRIS EIGER X 16M KB mirrors 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.367 51.59 99.97 0.09569 0.09834 0.02248 1 21.56 17.9 71319 14.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.367 1.416 99.9 1.328 1.4 0.4337 0.847 2.09 9.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5FNU 1.37 51.59 1.38 71305 3557 99.97 0.151 0.1498 0.1505 0.173 0.1745 Random 22.4
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 20.1649 f_angle_d 1.006 f_chiral_restr 0.09 f_bond_d 0.0071 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2235 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 73
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing PHENIX refinement