4GUJ

1.50 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Shikimate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5300protein: 7.5 mg/mL in 0.5 M sodium shikimate, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG II B8 (0.01 M nickel chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME), crystal incubated in and frozen from 2 M sodium shikimate, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.0439.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.62α = 90
b = 74.966β = 100.49
c = 63.042γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lens2012-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-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
11.53096.90.04525.53.96917569175-3
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)
11.51.5394.50.3673.83.93375

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 3L2I1.528.666544365443348396.850.156740.156740.155340.18237RANDOM20.966
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]
-1.961.7-0.321.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.58
r_dihedral_angle_4_deg13.25
r_dihedral_angle_3_deg9.8
r_dihedral_angle_1_deg3.547
r_angle_refined_deg1.421
r_angle_other_deg0.737
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.58
r_dihedral_angle_4_deg13.25
r_dihedral_angle_3_deg9.8
r_dihedral_angle_1_deg3.547
r_angle_refined_deg1.421
r_angle_other_deg0.737
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.006
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_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 Atoms3818
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms27

Software

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