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Crystal structure of the Keap1 protein in complexed with the N-terminal region of the Nrf2 transcription factor
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 VAPOR DIFFUSION, SITTING DROP 5.6 298 Ammonium sulfate, Lithium Sulfate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.131 α = 90 b = 103.131 β = 90 c = 56.141 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 103 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2005-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.9 50 98.2 0.086 8.6 27043 26542 -3
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) 1.9 1.97 88 0.398 3.6 2359
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X2J 1.9 20 25143 1335 98.2 0.17432 0.17237 0.21102 RANDOM 34.302
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] -0.8 -0.4 -0.8 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.524 r_dihedral_angle_4_deg 19.811 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 7.018 r_scangle_it 3.81 r_scbond_it 2.691 r_mcangle_it 1.808 r_angle_refined_deg 1.55 r_mcbond_it 1.142 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.524 r_dihedral_angle_4_deg 19.811 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 7.018 r_scangle_it 3.81 r_scbond_it 2.691 r_mcangle_it 1.808 r_angle_refined_deg 1.55 r_mcbond_it 1.142 r_nbtor_refined 0.304 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.218 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.118 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2321 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DNA data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing