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Crystal structure of N-[(4-methoxyphenyl)sulfonyl]-N-(4-{[(4-methoxyphenyl)sulfonyl]amino}naphthalen-1-yl)glycine bound to human Keap1 Kelch domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U6D PDB entry 1U6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 3.5-3.8 M sodium formate, pH 7
Crystal Properties Matthews coefficient Solvent content 3.07 59.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.36 α = 74.55 b = 75.543 β = 77.54 c = 97.947 γ = 67.48
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-300 2019-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 1.6 19.74 92 0.033 0.047 0.033 0.999 10.5 2 182432
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 1.6 1.63 94.3 0.463 0.654 0.463 0.665 2
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 PDB entry 1U6D 1.6 19.73 173224 9206 91.99 0.1927 0.1918 0.192 0.2104 0.2105 RANDOM 23.41
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] 1.36 0.11 -0.52 -0.77 0.37 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.628 r_dihedral_angle_4_deg 18.154 r_dihedral_angle_3_deg 11.717 r_dihedral_angle_1_deg 7.593 r_angle_refined_deg 1.44 r_chiral_restr 0.098 r_gen_planes_refined 0.008 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8747 Nucleic Acid Atoms Solvent Atoms 1047 Heterogen Atoms 359
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction