3ZV4

CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 IN APO FORM AT 1.8 ANGSTROM


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SODIUM MALONATE, PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2545.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.784α = 90
b = 75.784β = 90
c = 181.782γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.5810099.90.09137.173356226.701
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)
11.870.011000.881.447.3

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 1BDB1.870.0147247248999.440.192970.191130.22736RANDOM31.433
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]
-0.19-0.190.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.157
r_dihedral_angle_4_deg19.232
r_dihedral_angle_3_deg14.353
r_dihedral_angle_1_deg5.911
r_scangle_it1.96
r_scbond_it1.4
r_angle_refined_deg1.253
r_angle_other_deg0.938
r_mcangle_it0.721
r_mcbond_it0.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.157
r_dihedral_angle_4_deg19.232
r_dihedral_angle_3_deg14.353
r_dihedral_angle_1_deg5.911
r_scangle_it1.96
r_scbond_it1.4
r_angle_refined_deg1.253
r_angle_other_deg0.938
r_mcangle_it0.721
r_mcbond_it0.609
r_symmetry_vdw_other0.263
r_nbd_refined0.2
r_nbd_other0.193
r_nbtor_refined0.171
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.152
r_mcbond_other0.126
r_nbtor_other0.085
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3902
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing