5BUX

Crystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Yersinia pestis with glycerol bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZHGPDB entry 1ZHG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2938% Tacsimate, pH 8.0, 400 mM sodium thiocyanate, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.2762.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.76α = 90
b = 104.76β = 90
c = 87.961γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.07NSLSX29A

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
11.95097.80.05230.37.94236642366
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)
11.91.9684.50.07823

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1ZHG1.939.6140206214097.750.156910.155430.18534RANDOM22.887
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]
0.460.460.46-1.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_3_deg15.633
r_dihedral_angle_4_deg15.395
r_dihedral_angle_1_deg7.027
r_angle_refined_deg2.364
r_angle_other_deg0.998
r_chiral_restr0.166
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_3_deg15.633
r_dihedral_angle_4_deg15.395
r_dihedral_angle_1_deg7.027
r_angle_refined_deg2.364
r_angle_other_deg0.998
r_chiral_restr0.166
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2277
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing