3II9

Crystal structure of glutaryl-coa dehydrogenase from Burkholderia pseudomallei at 1.73 Angstrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D6BPDB Entry 3D6B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microfluidic microbatch8.529619.4% PEG 400, 43 mM Tris 8.5, 86 mM MgCl2, Microfluidic microbatch, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5752.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.966α = 90
b = 141.268β = 112.26
c = 84.012γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

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
11.735099.30.0453.817748522
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)
11.731.7998.60.9741.73.7

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 REPLACEMENTTHROUGHOUTPDB Entry 3D6B1.7440.23168491889798.750.171640.170370.19561RANDOM14.107
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]
-0.070.050.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.208
r_dihedral_angle_4_deg19.356
r_dihedral_angle_3_deg12.382
r_dihedral_angle_1_deg5.224
r_scangle_it3.378
r_scbond_it2.011
r_mcangle_it1.192
r_angle_refined_deg1.159
r_angle_other_deg0.852
r_mcbond_it0.604
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.208
r_dihedral_angle_4_deg19.356
r_dihedral_angle_3_deg12.382
r_dihedral_angle_1_deg5.224
r_scangle_it3.378
r_scbond_it2.011
r_mcangle_it1.192
r_angle_refined_deg1.159
r_angle_other_deg0.852
r_mcbond_it0.604
r_symmetry_vdw_refined0.354
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.15
r_mcbond_other0.146
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.005
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_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11785
Nucleic Acid Atoms
Solvent Atoms907
Heterogen Atoms121

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling