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Crystal structure of the Keap1 Kelch domain in complex with a tetrapeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 bis-tris, sodium formate
Crystal Properties Matthews coefficient Solvent content 3.35 63.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.566 α = 90 b = 75.705 β = 90 c = 168.132 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 270 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976486 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.3 50 98.7 0.15 0.06 0.996 12.3 7.2 39255
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.666 0.283 0.846 3.1 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1U6D 2.3 40 37219 1957 98.7 0.16933 0.16734 0.20808 0.1726 RANDOM 25.361
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] -1.48 1.34 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.219 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 7.206 r_long_range_B_refined 3.075 r_long_range_B_other 3.015 r_scangle_other 1.783 r_angle_refined_deg 1.432 r_mcangle_it 1.394 r_mcangle_other 1.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.219 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 7.206 r_long_range_B_refined 3.075 r_long_range_B_other 3.015 r_scangle_other 1.783 r_angle_refined_deg 1.432 r_mcangle_it 1.394 r_mcangle_other 1.394 r_scbond_it 1.036 r_scbond_other 1.035 r_angle_other_deg 0.979 r_mcbond_it 0.791 r_mcbond_other 0.79 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4498 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing