3S42

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L20PDB ENTRY 3L20

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.53000.5 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 coefficientSolvent content
1.8934.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.562α = 90
b = 72.569β = 90
c = 171.353γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lens2011-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.453099.60.06820.75.68185081850-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4895.20.2764.33.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3L201.4528.567760477604409199.630.145150.143520.17527RANDOM14.752
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]
-0.51.49-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.531
r_dihedral_angle_4_deg16.884
r_dihedral_angle_3_deg10.533
r_scangle_it5.225
r_dihedral_angle_1_deg3.612
r_scbond_it3.397
r_mcangle_it2.293
r_angle_refined_deg2.2
r_mcbond_it1.494
r_angle_other_deg1.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.531
r_dihedral_angle_4_deg16.884
r_dihedral_angle_3_deg10.533
r_scangle_it5.225
r_dihedral_angle_1_deg3.612
r_scbond_it3.397
r_mcangle_it2.293
r_angle_refined_deg2.2
r_mcbond_it1.494
r_angle_other_deg1.056
r_mcbond_other0.55
r_chiral_restr0.134
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms4026
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms48

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling