3NNT

Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Non-Covalent Complex with Dehydroquinate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LB0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3295Protein solution: 7.5 mG/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3, 2mM 3-Dehydroquinic acid (DHR); Screen solution: Classics F9, 0.05M Potassium phosphate, 20%(w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9637.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.727α = 91.18
b = 43.548β = 101.27
c = 79.938γ = 109.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2010-06-18MSINGLE 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
11.63096.70.0323.225859058590-324
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)
1.61.63950.3572.2522852

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 REPLACEMENTTHROUGHOUT3LB01.629.655540555405295096.750.159420.159420.15790.18749RANDOM19.535
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]
0.080.610.580.51-0.250.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.046
r_dihedral_angle_4_deg12.236
r_dihedral_angle_3_deg9.683
r_scangle_it4.498
r_dihedral_angle_1_deg3.362
r_scbond_it2.695
r_mcangle_it1.667
r_angle_refined_deg1.409
r_mcbond_it0.96
r_angle_other_deg0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.046
r_dihedral_angle_4_deg12.236
r_dihedral_angle_3_deg9.683
r_scangle_it4.498
r_dihedral_angle_1_deg3.362
r_scbond_it2.695
r_mcangle_it1.667
r_angle_refined_deg1.409
r_mcbond_it0.96
r_angle_other_deg0.85
r_mcbond_other0.271
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3922
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms26

Software

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