3ZV5

CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT 2,3-DIHYDROXYBIPHENYL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BDBPDB ENTRY 1BDB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SODIUM MALONATE, PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1342.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.394α = 90
b = 75.394β = 90
c = 173.567γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-07-14MSINGLE 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
12.3650950.119.3212.120162247.592
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)
12.469.1799.40.612.297.7

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 1BDB2.469.171814198294.180.210590.207620.26568RANDOM43.265
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]
1.681.68-3.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.95
r_dihedral_angle_4_deg20.136
r_dihedral_angle_3_deg19.538
r_dihedral_angle_1_deg6.497
r_scangle_it2.744
r_scbond_it1.803
r_angle_refined_deg1.776
r_mcangle_it1.014
r_mcbond_it0.619
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.95
r_dihedral_angle_4_deg20.136
r_dihedral_angle_3_deg19.538
r_dihedral_angle_1_deg6.497
r_scangle_it2.744
r_scbond_it1.803
r_angle_refined_deg1.776
r_mcangle_it1.014
r_mcbond_it0.619
r_nbtor_refined0.31
r_symmetry_vdw_refined0.241
r_nbd_refined0.228
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.163
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms3978
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms102

Software

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