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Crystal structure of Keap1 kelch domain in complex with a fluorenone-based small molecule inhibitor at 1.36A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OFE
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 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.119 α = 90 b = 103.119 β = 90 c = 55.266 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 2022-09-23 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 1.36 46.99 99.8 0.088 0.09 0.02 0.999 16.6 20.3 71819 20.97
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 1.36 1.41 99.6 2.65 2.725 0.628 0.639 18.4
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 1.36 44.65 1.35 71737 3623 99.76 0.1437 0.142 0.1444 0.1745 0.1768 28.32
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 6.694 f_angle_d 1.023 f_chiral_restr 0.092 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2235 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 120
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement