3DX5

Crystal structure of the probable 3-DHS dehydratase AsbF involved in the petrobactin synthesis from Bacillus anthracis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1M Tris pH8.5, 3.2 M soudium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8256.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.483α = 90
b = 134.483β = 90
c = 72.806γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-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
12.1149.499.90.1449.113.9227262272622.1
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)
12.112.1999.40.5346.712.32210

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 DIFFRACTIONSADTHROUGHOUT2.1249.42134221342115199.90.150.150.1480.178RANDOM16.061
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]
0.250.130.25-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.369
r_dihedral_angle_4_deg24.834
r_dihedral_angle_3_deg14.445
r_dihedral_angle_1_deg5.676
r_scangle_it4.023
r_scbond_it2.511
r_angle_refined_deg1.468
r_mcangle_it1.412
r_mcbond_it0.735
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.369
r_dihedral_angle_4_deg24.834
r_dihedral_angle_3_deg14.445
r_dihedral_angle_1_deg5.676
r_scangle_it4.023
r_scbond_it2.511
r_angle_refined_deg1.468
r_mcangle_it1.412
r_mcbond_it0.735
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.007
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 Atoms2250
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
Cootmodel building