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Keap1 kelch domain bound to a small molecule fragment
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 2.77 55.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.715 α = 90 b = 103.715 β = 90 c = 56.294 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 PILATUS 6M Toroidal Mirror 2018-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 ESRF ID29
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 1.378 44.91 99.98 0.07747 0.08392 0.03197 0.998 10.25 6.8 70870 18.38
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 1.38 1.43 99.91 0.7667 0.836 0.3299 0.562 1.25 6.3
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 1.38 44.91 1.49 70754 3539 99.8 0.1626 0.1616 0.1628 0.1811 0.1842 Random 30.8
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 17.3203 f_angle_d 0.8578 f_chiral_restr 0.0826 f_bond_d 0.0045 f_plane_restr 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 48
Software Software Software Name Purpose xia2 data reduction xia2 data scaling PHASER phasing PHENIX refinement