4GUG

1.62 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) E86A Mutant in Complex with Dehydroshikimate (Crystal Form #1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3300protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 3 mM dehydroquinic acid, crystallization condition: 0.19 M sodium chloride, 17.9% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
1.9837.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.703α = 90
b = 64.266β = 93.89
c = 81.045γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBimorph K-B pair2012-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97850APS21-ID-D

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
11.623097.20.05421.23.85784957849-3
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)
11.621.65950.5252.63.62802

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3L2I1.6229.865491654916290897.020.175310.175310.173490.20827RANDOM36.376
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]
1.042.091.17-2.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.668
r_dihedral_angle_4_deg17.149
r_dihedral_angle_3_deg11.983
r_dihedral_angle_1_deg4.216
r_angle_refined_deg1.971
r_angle_other_deg0.862
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.668
r_dihedral_angle_4_deg17.149
r_dihedral_angle_3_deg11.983
r_dihedral_angle_1_deg4.216
r_angle_refined_deg1.971
r_angle_other_deg0.862
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.01
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_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 AtomsNumber
Protein Atoms3750
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms24

Software

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