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Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium with close loop conformation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L2I PDB CODE 3L2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 Protein: 7.5mGr/mL, 0.5M Sodium Cloride, 0.01M TRIS-HCL pH 8.3, 1mM 3-DHSK;
Screen: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate pH 4.6, 25.5% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.02 39.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.147 α = 90 b = 75.757 β = 102.65 c = 94.263 γ = 90
Symmetry Space Group P 1 21 1
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 1.9 30 99.9 0.085 12.6 3.3 69261 69261 -3 18.1
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 1.93 99.7 0.389 2.8 2.7 3428
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 (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 CODE 3L2I 1.9 29.53 65729 65729 3507 99.75 0.15443 0.1518 0.1626 0.20366 0.2133 RANDOM 17.986
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] 1.02 0.5 -0.52 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 10.955 r_dihedral_angle_3_deg 10.629 r_scangle_it 4.79 r_dihedral_angle_1_deg 3.296 r_scbond_it 2.901 r_mcangle_it 1.819 r_angle_refined_deg 1.431 r_mcbond_it 1.062 r_angle_other_deg 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 10.955 r_dihedral_angle_3_deg 10.629 r_scangle_it 4.79 r_dihedral_angle_1_deg 3.296 r_scbond_it 2.901 r_mcangle_it 1.819 r_angle_refined_deg 1.431 r_mcbond_it 1.062 r_angle_other_deg 0.88 r_mcbond_other 0.313 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7649 Nucleic Acid Atoms Solvent Atoms 887 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling