☰ Navigation Tabs
1.78 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Quinate
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 8.5 300 protein: 7.5 mg/mL in 0.5 M sodium shikimate, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG II B8 (0.01 M nickel chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME), crystal incubated in and frozen from 5 M sodium quinate, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.03 39.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.669 α = 90 b = 74.427 β = 100.57 c = 63.135 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 lens 2012-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 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 1.78 30 97.2 0.056 17.5 3 41378 41378 -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 1.78 1.81 99.3 0.314 2.4 2.3 2109
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 1.78 28.66 39202 39202 2100 97.22 0.16079 0.16079 0.15927 0.1701 0.18801 0.1961 RANDOM 33.88
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 3.42 -0.35 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.743 r_dihedral_angle_4_deg 12.821 r_dihedral_angle_3_deg 9.917 r_dihedral_angle_1_deg 3.128 r_angle_refined_deg 1.351 r_angle_other_deg 0.727 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.743 r_dihedral_angle_4_deg 12.821 r_dihedral_angle_3_deg 9.917 r_dihedral_angle_1_deg 3.128 r_angle_refined_deg 1.351 r_angle_other_deg 0.727 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 3818 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 32
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling