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Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L20 PDB ENTRY 3L20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 300 0.5 M Sodium Chloride,
0.010 M Tris-HCl,
Qiagen PACT B2,
0.1 M MIB Buffer (containing 0.025 M Sodium Malonate, 0.037 M Boric Acid, 0.025 M Imidazole),
25% (w/v) PEG 1500, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.89 34.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.562 α = 90 b = 72.569 β = 90 c = 171.353 γ = 90
Symmetry Space Group P 21 21 21
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 225 mm CCD Beryllium lens 2011-04-21 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 1.45 30 99.6 0.068 20.7 5.6 81850 81850 -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 1.45 1.48 95.2 0.276 4.3 3.4
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 ENTRY 3L20 1.45 28.56 77604 77604 4091 99.63 0.14515 0.14352 0.1537 0.17527 0.182 RANDOM 14.752
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] -0.5 1.49 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.531 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 10.533 r_scangle_it 5.225 r_dihedral_angle_1_deg 3.612 r_scbond_it 3.397 r_mcangle_it 2.293 r_angle_refined_deg 2.2 r_mcbond_it 1.494 r_angle_other_deg 1.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.531 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 10.533 r_scangle_it 5.225 r_dihedral_angle_1_deg 3.612 r_scbond_it 3.397 r_mcangle_it 2.293 r_angle_refined_deg 2.2 r_mcbond_it 1.494 r_angle_other_deg 1.056 r_mcbond_other 0.55 r_chiral_restr 0.134 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4026 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 48
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling