2OG1

Crystal Structure of BphD, a C-C hydrolase from Burkholderia xenovorans LB400


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22932.0-2.4 M ammonium sulfate, 6-10% ethanol, 0.1M Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7554.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135α = 90
b = 135β = 90
c = 66.725γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 11998-09-18MSINGLE WAVELENGTH
21x-rayCCDADSC QUANTUM 11998-12-05MMAD
31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-DAPS14-BM-D
2SYNCHROTRONAPS BEAMLINE 14-BM-D0.9537,0.9793,0.9795APS14-BM-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
1,21.65096.60.069.988125
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)
1,21.61.6374.10.363352

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.619.8788125885696.60.2080.224RANDOM27.1
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]
0.321.250.32-0.64
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_scangle_it2.72
c_mcangle_it1.77
c_scbond_it1.76
c_angle_deg1.2
c_mcbond_it1.12
c_improper_angle_d0.7
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4492
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms35

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection