3LWZ

1.65 Angstrom Resolution Crystal Structure of Type II 3-Dehydroquinate Dehydratase (aroQ) from Yersinia pestis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein solution: 5.3 mg/mL, 0.5M Sodium chloride, 0.01M TRIS-HCl pH 8.3; Screen solution: ANL-2, D1, 0.17M Sodim Acetate, 0.085M TRIS HCl pH 8.5, 25.5% PEG 4000, 15% Glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5651.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.587α = 90
b = 90.587β = 90
c = 216.5γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2010-02-10MSINGLE 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
11.653099.90.05720.43.87978079780-322.1
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)
1.651.6898.50.3672.62.83916

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 REPLACEMENTTHROUGHOUT1UQR1.6529.387560775607399199.890.150680.150680.149030.18186RANDOM20.511
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]
1.140.571.14-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.42
r_dihedral_angle_3_deg11.035
r_dihedral_angle_4_deg10.323
r_dihedral_angle_1_deg4.357
r_scangle_it4.336
r_scbond_it2.791
r_mcangle_it2.097
r_angle_refined_deg1.319
r_mcbond_it1.232
r_angle_other_deg0.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.42
r_dihedral_angle_3_deg11.035
r_dihedral_angle_4_deg10.323
r_dihedral_angle_1_deg4.357
r_scangle_it4.336
r_scbond_it2.791
r_mcangle_it2.097
r_angle_refined_deg1.319
r_mcbond_it1.232
r_angle_other_deg0.869
r_mcbond_other0.34
r_chiral_restr0.086
r_bond_refined_d0.012
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 Atoms4908
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms122

Software

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