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Crystal structure of Keap1 complexed with Prothymosin alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X2J PDN ENTRY 1X2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Ammonium sulfate, Li2SO4, Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.515 α = 90 b = 103.515 β = 90 c = 56.16 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 CCD ADSC QUANTUM 315 mirrors 2006-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2 50 93.1 0.074 10.6 23352 21733 -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) 2 2.07 99.8 0.228 10.3 2299
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 PDN ENTRY 1X2J 2 20 20530 1119 92.9 0.16879 0.16598 0.1679 0.22317 0.2239 RANDOM 33.266
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] -1.66 -0.83 -1.66 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.088 r_dihedral_angle_4_deg 24.759 r_dihedral_angle_3_deg 14.226 r_dihedral_angle_1_deg 7.41 r_scangle_it 4.236 r_scbond_it 2.815 r_mcangle_it 2.021 r_angle_refined_deg 1.619 r_mcbond_it 1.253 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.088 r_dihedral_angle_4_deg 24.759 r_dihedral_angle_3_deg 14.226 r_dihedral_angle_1_deg 7.41 r_scangle_it 4.236 r_scbond_it 2.815 r_mcangle_it 2.021 r_angle_refined_deg 1.619 r_mcbond_it 1.253 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.25 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.122 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2316 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing