3KAO

Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528910 mM zinc sulfate, 100 mM MES pH 6.5, 12.5 % PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
4.974.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.704α = 90
b = 84.704β = 90
c = 202.759γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97931APS19-ID

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
11.95099.90.0954.712.15908059016-324
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)
11.91.931000.4846.4311.82889

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.9505891758917298499.880.149350.149350.148210.17098RANDOM19.146
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]
-0.24-0.240.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.368
r_dihedral_angle_3_deg13.467
r_dihedral_angle_4_deg12.959
r_dihedral_angle_1_deg5.532
r_scangle_it3.595
r_scbond_it2.145
r_angle_refined_deg1.224
r_mcangle_it1.097
r_mcbond_it0.59
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.368
r_dihedral_angle_3_deg13.467
r_dihedral_angle_4_deg12.959
r_dihedral_angle_1_deg5.532
r_scangle_it3.595
r_scbond_it2.145
r_angle_refined_deg1.224
r_mcangle_it1.097
r_mcbond_it0.59
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 Atoms2569
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms36

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing