3D6B

2.2 A crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.528920% PEG 3000, 0.1M HEPES pH 7.5, 0.2M NaCl, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2144.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.503α = 90
b = 107.472β = 90
c = 144.313γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUSING MIRRORS2008-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.00000APS23-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
12.25099.60.1058.5776333
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)
12.22.2897.70.7485.77400

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 REPLACEMENTTHROUGHOUT2.2147.1976240382698.790.2120.2090.261RANDOM36.451
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.309
r_dihedral_angle_4_deg21.13
r_dihedral_angle_3_deg16.343
r_dihedral_angle_1_deg5.471
r_scangle_it2.21
r_scbond_it1.388
r_angle_refined_deg1.24
r_mcangle_it1.074
r_mcbond_it0.624
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.309
r_dihedral_angle_4_deg21.13
r_dihedral_angle_3_deg16.343
r_dihedral_angle_1_deg5.471
r_scangle_it2.21
r_scbond_it1.388
r_angle_refined_deg1.24
r_mcangle_it1.074
r_mcbond_it0.624
r_nbtor_refined0.297
r_symmetry_vdw_refined0.241
r_symmetry_hbond_refined0.225
r_nbd_refined0.199
r_xyhbond_nbd_refined0.157
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11436
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms9

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling