3V1L

Crystal Structure of the S112A/H265Q mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSING, SITTING DROP, MICROSEEDING6.82982.4 M Sodium malonate, pH 6.8, VAPOR DIFFUSING, SITTING DROP, MICROSEEDING, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3647.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.458α = 90
b = 117.458β = 90
c = 87.791γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033APS23-ID-B

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
12.1183.0697.80.12677.617692
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)
12.112.1980.60.3673.21432

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 REPLACEMENTTHROUGHOUT2.1183.061766989398.660.18090.17890.2188RANDOM24.0162
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]
0.740.74-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.636
r_dihedral_angle_4_deg20.397
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg5.643
r_angle_refined_deg1.261
r_angle_other_deg0.861
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.636
r_dihedral_angle_4_deg20.397
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg5.643
r_angle_refined_deg1.261
r_angle_other_deg0.861
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2238
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms7

Software

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