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1.62 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) E86A Mutant in Complex with Dehydroshikimate (Crystal Form #1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L2I PDB ENTRY 3L2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 300 protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 3 mM dehydroquinic acid, crystallization condition: 0.19 M sodium chloride, 17.9% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.98 37.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.703 α = 90 b = 64.266 β = 93.89 c = 81.045 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 Bimorph K-B pair 2012-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97850 APS 21-ID-D
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 1.62 30 97.2 0.054 21.2 3.8 57849 57849 -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) 1 1.62 1.65 95 0.525 2.6 3.6 2802
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 PDB ENTRY 3L2I 1.62 29.86 54916 54916 2908 97.02 0.17531 0.17531 0.17349 0.1835 0.20827 0.2146 RANDOM 36.376
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] 1.04 2.09 1.17 -2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.668 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 11.983 r_dihedral_angle_1_deg 4.216 r_angle_refined_deg 1.971 r_angle_other_deg 0.862 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.668 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 11.983 r_dihedral_angle_1_deg 4.216 r_angle_refined_deg 1.971 r_angle_other_deg 0.862 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3750 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 24
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling