5B6P

Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter baumannii at 2.00 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829830% PEG 3350, MgSO4, Tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.284α = 90
b = 95.279β = 95.73
c = 132.263γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2014-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12131.696.20.09317.612942722.8
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)
122.031000.4414.67.7

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 REPLACEMENTTHROUGHOUT3LWZ2131.6129427158896.20.200980.200590.23215RANDOM29.142
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]
0.63-0.090.09-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.781
r_dihedral_angle_3_deg14.775
r_dihedral_angle_4_deg11.453
r_long_range_B_refined7.812
r_long_range_B_other7.811
r_dihedral_angle_1_deg6.262
r_scangle_other5.547
r_mcangle_it4.625
r_mcangle_other4.625
r_scbond_it3.563
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.781
r_dihedral_angle_3_deg14.775
r_dihedral_angle_4_deg11.453
r_long_range_B_refined7.812
r_long_range_B_other7.811
r_dihedral_angle_1_deg6.262
r_scangle_other5.547
r_mcangle_it4.625
r_mcangle_other4.625
r_scbond_it3.563
r_scbond_other3.56
r_mcbond_it3.052
r_mcbond_other3.047
r_angle_other_deg2.482
r_angle_refined_deg1.909
r_chiral_restr0.157
r_bond_refined_d0.02
r_bond_other_d0.016
r_gen_planes_refined0.013
r_gen_planes_other0.011
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 Atoms13452
Nucleic Acid Atoms
Solvent Atoms769
Heterogen Atoms60

Software

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