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1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium
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 8.5 295 Protein: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen: Classics II (H1), 0.2M Magnesium chloride, 0.1M Tris, pH 8.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.85 33.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.433 α = 104.23 b = 46.476 β = 97.5 c = 55.79 γ = 98.7
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 2010-04-22 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 1.03 30 92.7 0.068 15 4.3 196964 196964 -3 10.2
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) 1.03 1.05 84.9 0.333 3.7 3.4 8952
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 1.03 26.62 187094 187094 9868 92.63 0.14132 0.14132 0.14024 0.147 0.16161 0.1682 RANDOM 10.933
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] -0.62 0.61 -0.79 1.22 -0.89 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.151 r_dihedral_angle_4_deg 13.106 r_dihedral_angle_3_deg 10.697 r_dihedral_angle_1_deg 5.494 r_scangle_it 4.922 r_scbond_it 3.419 r_mcangle_it 2.482 r_mcbond_it 1.696 r_angle_refined_deg 1.464 r_rigid_bond_restr 1.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.151 r_dihedral_angle_4_deg 13.106 r_dihedral_angle_3_deg 10.697 r_dihedral_angle_1_deg 5.494 r_scangle_it 4.922 r_scbond_it 3.419 r_mcangle_it 2.482 r_mcbond_it 1.696 r_angle_refined_deg 1.464 r_rigid_bond_restr 1.445 r_angle_other_deg 0.886 r_mcbond_other 0.638 r_chiral_restr 0.09 r_bond_refined_d 0.012 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 3785 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling