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Structure of the Keap1 Kelch domain in complex with a small molecule inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X2J PDB ENTRY 1X2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.3-0.6 (NH4)2SO4, 0.4-1.4 M LI2SO4 AND 0.1 M NA3CITRATE-HCL PH 5.6
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.297 α = 90 b = 103.297 β = 90 c = 56.434 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 93 CCD RIGAKU CCD 2013-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+
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 1.78 51.65 87.5 0.04 18.7 2.2 28698
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 1.78 1.84 44.1 0.19 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X2J 1.78 51.65 27225 1473 87.5 0.16807 0.16608 0.1679 0.20487 0.2073 RANDOM 21.563
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 -0.05 -0.09 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.85 r_dihedral_angle_4_deg 16.767 r_dihedral_angle_3_deg 14.072 r_dihedral_angle_1_deg 7.164 r_scbond_it 1.803 r_angle_refined_deg 1.439 r_mcbond_it 0.781 r_angle_other_deg 0.17 r_chiral_restr 0.101 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.85 r_dihedral_angle_4_deg 16.767 r_dihedral_angle_3_deg 14.072 r_dihedral_angle_1_deg 7.164 r_scbond_it 1.803 r_angle_refined_deg 1.439 r_mcbond_it 0.781 r_angle_other_deg 0.17 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_bond_other_d 0.002 r_gen_planes_refined 0.001 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_it r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 2215 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling