3QBE

Crystal structure of the 3-Dehydroquinate Synthase (aroB) from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.8M sodium formate, 20% PEG 2000 MME, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.318α = 90
b = 140.318β = 90
c = 38.408γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315r2010-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.00000NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.0799.2299.80.0710.07122.55.7232282318611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.1499.70.4920.4923.655.42309

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3QBD2.07302322821996119099.750.203760.201350.24806RANDOM30.514
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]
-0.3-0.30.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.233
r_dihedral_angle_4_deg18.111
r_dihedral_angle_3_deg12.839
r_scangle_it5.654
r_dihedral_angle_1_deg3.66
r_scbond_it3.522
r_mcangle_it2.399
r_angle_refined_deg1.97
r_mcbond_it1.45
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.233
r_dihedral_angle_4_deg18.111
r_dihedral_angle_3_deg12.839
r_scangle_it5.654
r_dihedral_angle_1_deg3.66
r_scbond_it3.522
r_mcangle_it2.399
r_angle_refined_deg1.97
r_mcbond_it1.45
r_chiral_restr0.145
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2605
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms3

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling