5HPQ

Crystal structure of cyclohexadienyl dehydratase from Pseudomonas aeruginosa bound to acetate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KBR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22911 uL 10 mg/mL protein (20 mM TRIS pH 8.0, 100 mM NaCl, 0.5 mM DTT, 10% glycerol) + 1 uL 18% PEG 3350, 0.2 M ammonium acetate, 0.1 M TRIS pH 8.2
Crystal Properties
Matthews coefficientSolvent content
2.0840.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.89α = 90
b = 124.89β = 90
c = 40.63γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2014-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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
12.0538.0397.90.118.34.81447125.7
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)
12.052.1182.30.5791.62.5

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 REPLACEMENTTHROUGHOUT3KBR2.0536.051373972797.880.179130.175890.24099RANDOM30.129
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.581
r_dihedral_angle_4_deg21.685
r_dihedral_angle_3_deg14.447
r_dihedral_angle_1_deg7.426
r_long_range_B_refined5.872
r_long_range_B_other5.845
r_scangle_other4.415
r_mcangle_other3.679
r_mcangle_it3.672
r_scbond_it2.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.581
r_dihedral_angle_4_deg21.685
r_dihedral_angle_3_deg14.447
r_dihedral_angle_1_deg7.426
r_long_range_B_refined5.872
r_long_range_B_other5.845
r_scangle_other4.415
r_mcangle_other3.679
r_mcangle_it3.672
r_scbond_it2.981
r_scbond_other2.979
r_mcbond_it2.58
r_mcbond_other2.553
r_angle_refined_deg1.781
r_angle_other_deg0.883
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.01
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1870
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing