3LB0

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Citrate Bound to the Active Site.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2295Protein solution:7.5 mG/mL, 0.01M Comenic acid, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3) Screen solution: JCSG+ (condition 25), 0.2M Sodium Chloride, 0.1M Phosphate-citrate (pH 4.2), 20% w/v PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1342.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.888α = 93.95
b = 45.853β = 101.19
c = 80.816γ = 105.49
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDberyllium lenses2009-12-21MSINGLE 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
11.653093.90.03321.225611756117-318.8
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)
1.651.6895.40.135.51.82889

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 REPLACEMENTTHROUGHOUT3L2I1.6526.35325553255282993.860.162490.162490.160480.20071RANDOM17.109
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]
-0.090.75-0.122.01-0.04-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.065
r_dihedral_angle_4_deg14.159
r_dihedral_angle_3_deg10.149
r_scangle_it4.833
r_dihedral_angle_1_deg3.505
r_scbond_it2.939
r_mcangle_it1.948
r_angle_refined_deg1.471
r_mcbond_it1.145
r_angle_other_deg0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.065
r_dihedral_angle_4_deg14.159
r_dihedral_angle_3_deg10.149
r_scangle_it4.833
r_dihedral_angle_1_deg3.505
r_scbond_it2.939
r_mcangle_it1.948
r_angle_refined_deg1.471
r_mcbond_it1.145
r_angle_other_deg0.899
r_mcbond_other0.337
r_chiral_restr0.091
r_bond_refined_d0.013
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 Atoms4333
Nucleic Acid Atoms
Solvent Atoms600
Heterogen Atoms24

Software

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