5YDB

Crystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter baumannii with dehydroquinic acid at 1.76 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B6P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.05M Cadmium sulfate hydrate, 0.1M HEPES, PH 7.5, IM Sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
2.3347.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.117α = 90
b = 139.117β = 90
c = 79.587γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.97ESRFMASSIF-3

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
11.7669.5698.38.22.856929
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.8298.80.72.8

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 REPLACEMENTTHROUGHOUT5B6P1.7669.5653283266698.280.199260.197230.24766RANDOM48.171
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]
-0.4-0.2-0.41.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.127
r_dihedral_angle_3_deg17.45
r_dihedral_angle_4_deg10.506
r_long_range_B_refined9.909
r_long_range_B_other9.909
r_dihedral_angle_1_deg6.512
r_scangle_other5.501
r_mcangle_it4.832
r_mcangle_other4.831
r_scbond_it3.718
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.127
r_dihedral_angle_3_deg17.45
r_dihedral_angle_4_deg10.506
r_long_range_B_refined9.909
r_long_range_B_other9.909
r_dihedral_angle_1_deg6.512
r_scangle_other5.501
r_mcangle_it4.832
r_mcangle_other4.831
r_scbond_it3.718
r_scbond_other3.714
r_mcbond_it3.128
r_mcbond_other3.122
r_angle_refined_deg2.153
r_angle_other_deg1.222
r_chiral_restr0.154
r_bond_refined_d0.024
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms4484
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms56

Software

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