3EKZ

Structural Characterization of tetrameric Mycobacterium tuberculosis fructose 1,6-bisphosphate aldolase - substrate binding and catalysis mechanism of a class IIa bacterial aldolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EKLPDB ENTRY 3EKL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.829826% PEG 300, 0.1 NaAcetate pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.0669.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.22α = 90
b = 120.486β = 90
c = 164.327γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0797.197.53665536655
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.072.1488.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3EKL2.0725.93664836648183897.410.159090.157940.18014RANDOM20.638
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]
1.96-0.8-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_dihedral_angle_3_deg15.721
r_dihedral_angle_1_deg11.042
r_dihedral_angle_4_deg10.69
r_scangle_it3.352
r_scbond_it2.099
r_angle_refined_deg1.666
r_mcangle_it1.068
r_mcbond_it0.609
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_dihedral_angle_3_deg15.721
r_dihedral_angle_1_deg11.042
r_dihedral_angle_4_deg10.69
r_scangle_it3.352
r_scbond_it2.099
r_angle_refined_deg1.666
r_mcangle_it1.068
r_mcbond_it0.609
r_nbtor_refined0.3
r_chiral_restr0.251
r_nbd_refined0.21
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.14
r_metal_ion_refined0.092
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2578
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms33

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling