3GQT

Crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei with fragment (1,4-dimethyl-1,2,3,4-tetrahydroquinoxalin-6-yl)methylamine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.528920% PEG 3000, 0.1M HEPES pH 7.5, 0.2M NaCl. Soaked overnight with 25 mM (1,4-dimethyl-1,2,3,4-tetrahydroquinoxalin-6-yl)methylamine, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1642.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.418α = 90
b = 106.374β = 90
c = 144.774γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.97ALS5.0.3

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
11.99501000.07310.17.2103621
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)
11.992.061000.6866.1

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 3D6B1.995010347351750.2020.20.238RANDOM38.32
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]
0.52-0.45-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.916
r_dihedral_angle_4_deg20.856
r_dihedral_angle_3_deg14.48
r_dihedral_angle_1_deg5.572
r_scangle_it3.801
r_scbond_it2.377
r_mcangle_it1.519
r_angle_refined_deg1.431
r_mcbond_it0.84
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.916
r_dihedral_angle_4_deg20.856
r_dihedral_angle_3_deg14.48
r_dihedral_angle_1_deg5.572
r_scangle_it3.801
r_scbond_it2.377
r_mcangle_it1.519
r_angle_refined_deg1.431
r_mcbond_it0.84
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11525
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms42

Software

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