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Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Non-Covalent Complex with Dehydroquinate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3 295 Protein solution: 7.5 mG/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3, 2mM 3-Dehydroquinic acid (DHR);
Screen solution: Classics F9, 0.05M Potassium phosphate, 20%(w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.96 37.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.727 α = 91.18 b = 43.548 β = 101.27 c = 79.938 γ = 109.05
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 MARMOSAIC 300 mm CCD Beryllium lenses 2010-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.6 30 96.7 0.03 23.2 2 58590 58590 -3 24
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) 1.6 1.63 95 0.357 2.25 2 2852
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3LB0 1.6 29.65 55405 55405 2950 96.75 0.15942 0.15942 0.1579 0.18749 0.2101 RANDOM 19.535
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] 0.08 0.61 0.58 0.51 -0.25 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.046 r_dihedral_angle_4_deg 12.236 r_dihedral_angle_3_deg 9.683 r_scangle_it 4.498 r_dihedral_angle_1_deg 3.362 r_scbond_it 2.695 r_mcangle_it 1.667 r_angle_refined_deg 1.409 r_mcbond_it 0.96 r_angle_other_deg 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.046 r_dihedral_angle_4_deg 12.236 r_dihedral_angle_3_deg 9.683 r_scangle_it 4.498 r_dihedral_angle_1_deg 3.362 r_scbond_it 2.695 r_mcangle_it 1.667 r_angle_refined_deg 1.409 r_mcbond_it 0.96 r_angle_other_deg 0.85 r_mcbond_other 0.271 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3922 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 26
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling