3L2I

1.85 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GQN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3295Protein solution: 7.5 mG/mL, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2, drop D3; 0.2M Magnesium Chloride, 20% PEG 3350. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0339.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.919α = 90
b = 76.909β = 90
c = 171.854γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2009-12-10MSINGLE 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
11.85301000.07721.36.54286142861-321.1
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)
1.851.8899.80.3554.14.52081

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 REPLACEMENTTHROUGHOUT1GQN1.8528.644064640646214199.880.169820.169820.167530.21384RANDOM17.923
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]
-1.020.710.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.64
r_dihedral_angle_4_deg13.483
r_dihedral_angle_3_deg10.942
r_scangle_it5.562
r_dihedral_angle_1_deg3.588
r_scbond_it3.309
r_mcangle_it2.154
r_angle_refined_deg1.526
r_mcbond_it1.201
r_angle_other_deg0.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.64
r_dihedral_angle_4_deg13.483
r_dihedral_angle_3_deg10.942
r_scangle_it5.562
r_dihedral_angle_1_deg3.588
r_scbond_it3.309
r_mcangle_it2.154
r_angle_refined_deg1.526
r_mcbond_it1.201
r_angle_other_deg0.926
r_mcbond_other0.331
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3895
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms1

Software

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