3M7W

Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Covalent Complex with Dehydroquinate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6295Protein solution: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate (pH 4.6), 25.5% PEG 4000, 15% Glycerol; Soak: 5mM Dehydroquinic acid in screen solution for 20 min., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0740.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.334α = 90
b = 66.576β = 119.08
c = 128.23γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBERYLLIUM LENSES2010-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

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
11.95301000.08614.93.799121-320.2
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)
1.952.021000.4662.83.6

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 REPLACEMENTTHROUGHOUT3L2I1.9529.699416794167494299.90.1570.1540.206RANDOM20.01
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]
1.711.6-1.441.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.909
r_dihedral_angle_4_deg11.719
r_dihedral_angle_3_deg10.061
r_scangle_it4.994
r_scbond_it3.07
r_dihedral_angle_1_deg3.054
r_mcangle_it1.936
r_angle_refined_deg1.447
r_mcbond_it1.137
r_angle_other_deg0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.909
r_dihedral_angle_4_deg11.719
r_dihedral_angle_3_deg10.061
r_scangle_it4.994
r_scbond_it3.07
r_dihedral_angle_1_deg3.054
r_mcangle_it1.936
r_angle_refined_deg1.447
r_mcbond_it1.137
r_angle_other_deg0.862
r_mcbond_other0.346
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms11462
Nucleic Acid Atoms
Solvent Atoms1108
Heterogen Atoms156

Software

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