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Human Kelch like-ECH Associated Protein 1 (Keap1)
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 8.5 277 4.0 M Ammonium acetate, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 5 75.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.644 α = 90 b = 75.825 β = 90 c = 218.656 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 298 PIXEL RIGAKU HyPix-3000 2023-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 31.15 99.76 0.01 2.07 10 25899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.01 3.02 97.9 0.992
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 31.15 23737 2162 99.62 0.2754 0.2754 0.2996 0.3291 0.3039 RANDOM 58.83
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] -0.09 -0.01 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.146 r_long_range_B_refined 14.247 r_mcangle_it 8.617 r_dihedral_angle_1_deg 7.41 r_mcbond_it 5.117 r_dihedral_angle_2_deg 5.037 r_scbond_it 5.015 r_angle_refined_deg 1.363 r_chiral_restr 0.106 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.146 r_long_range_B_refined 14.247 r_mcangle_it 8.617 r_dihedral_angle_1_deg 7.41 r_mcbond_it 5.117 r_dihedral_angle_2_deg 5.037 r_scbond_it 5.015 r_angle_refined_deg 1.363 r_chiral_restr 0.106 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4362 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction PHASER phasing