3OEX

Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium with close loop conformation.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L2IPDB CODE 3L2I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6295Protein: 7.5mGr/mL, 0.5M Sodium Cloride, 0.01M TRIS-HCL pH 8.3, 1mM 3-DHSK; Screen: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate pH 4.6, 25.5% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0239.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.147α = 90
b = 75.757β = 102.65
c = 94.263γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2009-12-21MSINGLE 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
11.93099.90.08512.63.36926169261-318.1
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)
1.91.9399.70.3892.82.73428

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 CODE 3L2I1.929.536572965729350799.750.154430.15180.20366RANDOM17.986
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]
1.020.5-0.52-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.055
r_dihedral_angle_4_deg10.955
r_dihedral_angle_3_deg10.629
r_scangle_it4.79
r_dihedral_angle_1_deg3.296
r_scbond_it2.901
r_mcangle_it1.819
r_angle_refined_deg1.431
r_mcbond_it1.062
r_angle_other_deg0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.055
r_dihedral_angle_4_deg10.955
r_dihedral_angle_3_deg10.629
r_scangle_it4.79
r_dihedral_angle_1_deg3.296
r_scbond_it2.901
r_mcangle_it1.819
r_angle_refined_deg1.431
r_mcbond_it1.062
r_angle_other_deg0.88
r_mcbond_other0.313
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7649
Nucleic Acid Atoms
Solvent Atoms887
Heterogen Atoms4

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling