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Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Citrate Bound to the Active Site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 295 Protein solution:7.5 mG/mL, 0.01M Comenic acid, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3)
Screen solution: JCSG+ (condition 25), 0.2M Sodium Chloride, 0.1M Phosphate-citrate (pH 4.2), 20% w/v PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.888 α = 93.95 b = 45.853 β = 101.19 c = 80.816 γ = 105.49
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 2009-12-21 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 1.65 30 93.9 0.033 21.2 2 56117 56117 -3 18.8
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) 1.65 1.68 95.4 0.13 5.5 1.8 2889
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3L2I 1.65 26.3 53255 53255 2829 93.86 0.16249 0.16249 0.16048 0.1694 0.20071 0.2095 RANDOM 17.109
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 0.75 -0.12 2.01 -0.04 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.065 r_dihedral_angle_4_deg 14.159 r_dihedral_angle_3_deg 10.149 r_scangle_it 4.833 r_dihedral_angle_1_deg 3.505 r_scbond_it 2.939 r_mcangle_it 1.948 r_angle_refined_deg 1.471 r_mcbond_it 1.145 r_angle_other_deg 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.065 r_dihedral_angle_4_deg 14.159 r_dihedral_angle_3_deg 10.149 r_scangle_it 4.833 r_dihedral_angle_1_deg 3.505 r_scbond_it 2.939 r_mcangle_it 1.948 r_angle_refined_deg 1.471 r_mcbond_it 1.145 r_angle_other_deg 0.899 r_mcbond_other 0.337 r_chiral_restr 0.091 r_bond_refined_d 0.013 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 4333 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 24
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling