8IQ8

Crystal structure of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (DHPAO) from Acinetobacter baumannii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-A0A0H3GHT6-F1-model_v2sequence from KpHPAC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH42980.1 M PCB buffer pH4 and 25% w/v PEG1500 (Hampton Research kit)
Crystal Properties
Matthews coefficientSolvent content
3.0860.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.433α = 90
b = 62.84β = 90.09
c = 135.952γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSBRUKER PHOTON 1002017-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER TURBO X-RAY SOURCE1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.7721.0397.70.0970.1090.0470.99311.44.5147453
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8178.50.1690.2260.1490.921.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.821.041264941429096.180.228050.225010.25463RANDOM8.843
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]
0.01-0.03-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.104
r_dihedral_angle_4_deg18.435
r_dihedral_angle_3_deg13.202
r_dihedral_angle_1_deg6.907
r_long_range_B_refined3.416
r_long_range_B_other3.223
r_scangle_other1.901
r_angle_refined_deg1.487
r_mcangle_it1.393
r_mcangle_other1.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.104
r_dihedral_angle_4_deg18.435
r_dihedral_angle_3_deg13.202
r_dihedral_angle_1_deg6.907
r_long_range_B_refined3.416
r_long_range_B_other3.223
r_scangle_other1.901
r_angle_refined_deg1.487
r_mcangle_it1.393
r_mcangle_other1.393
r_angle_other_deg1.356
r_scbond_it1.152
r_scbond_other1.152
r_mcbond_it0.797
r_mcbond_other0.797
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms9000
Nucleic Acid Atoms
Solvent Atoms907
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PROTEUM PLUSdata reduction