2GBW

Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NDOPDB ENTRY 1NDO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8277.1520% PEG3350, 1.0 M Sodium Chloride, 0.037M Zinc Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.6854.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.958α = 90
b = 134.958β = 90
c = 219.887γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00000APS17-ID

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
11.719.895.30.0838.24.48253570241600
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)
11.71.7698.10.3942.94.1

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 1NDO1.719.82535702292471218095.220.190120.18810.2283RANDOM28.962
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.181
r_dihedral_angle_4_deg15.322
r_dihedral_angle_3_deg13.986
r_dihedral_angle_1_deg6.845
r_scangle_it3.476
r_scbond_it2.544
r_angle_refined_deg1.629
r_mcangle_it1.527
r_mcbond_it1.312
r_angle_other_deg0.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.181
r_dihedral_angle_4_deg15.322
r_dihedral_angle_3_deg13.986
r_dihedral_angle_1_deg6.845
r_scangle_it3.476
r_scbond_it2.544
r_angle_refined_deg1.629
r_mcangle_it1.527
r_mcbond_it1.312
r_angle_other_deg0.968
r_mcbond_other0.293
r_metal_ion_refined0.237
r_symmetry_vdw_other0.231
r_symmetry_hbond_refined0.222
r_nbd_other0.211
r_nbd_refined0.209
r_symmetry_vdw_refined0.203
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.179
r_chiral_restr0.102
r_nbtor_other0.085
r_xyhbond_nbd_other0.041
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14987
Nucleic Acid Atoms
Solvent Atoms1978
Heterogen Atoms21

Software

Software
Software NamePurpose
d*TREKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection