2PUH

Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with its substrate HOPDA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OG1PDB ENTRY 2OG1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.9 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.808α = 90
b = 116.808β = 90
c = 87.589γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.00APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.8282.599.35.436.67.82721322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.86894.345.12.65.72538

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2OG11.8282.482582527193136899.340.170.1680.203RANDOM31.5
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]
0.720.72-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.903
r_dihedral_angle_4_deg16.375
r_scangle_it14.384
r_dihedral_angle_3_deg13.803
r_scbond_it12.169
r_mcangle_it8.277
r_mcbond_it6.488
r_dihedral_angle_1_deg5.651
r_angle_refined_deg1.312
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.903
r_dihedral_angle_4_deg16.375
r_scangle_it14.384
r_dihedral_angle_3_deg13.803
r_scbond_it12.169
r_mcangle_it8.277
r_mcbond_it6.488
r_dihedral_angle_1_deg5.651
r_angle_refined_deg1.312
r_nbtor_refined0.311
r_symmetry_vdw_refined0.228
r_symmetry_hbond_refined0.223
r_nbd_refined0.207
r_xyhbond_nbd_refined0.116
r_symmetry_metal_ion_refined0.116
r_chiral_restr0.093
r_metal_ion_refined0.086
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2239
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing