2BMQ

The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BMOPDB ENTRY 2BMO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M HEPES PH 6.5, 6% PEG 8000 (W/V), 5MM NISO4, 50 MM NITROBENZENE. THE NITROBENZENE WAS PREPARED FROM A 1M STOCKSOLUTION WHERE NITROBENZENE WAS DISOLVED IN ETHANOL.
Crystal Properties
Matthews coefficientSolvent content
2.1542.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.533α = 90
b = 121.533β = 90
c = 84.179γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
11.5527.6398.50.086.75.1999641
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)
11.551.6399.70.511.44.3

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 2BMO1.552795726505098.50.1690.1670.192RANDOM17.71
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]
-0.44-0.22-0.440.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_4_deg17.613
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg6.234
r_scangle_it2.55
r_scbond_it1.779
r_angle_refined_deg1.306
r_mcangle_it1.095
r_mcbond_it0.658
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_4_deg17.613
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg6.234
r_scangle_it2.55
r_scbond_it1.779
r_angle_refined_deg1.306
r_mcangle_it1.095
r_mcbond_it0.658
r_nbtor_refined0.308
r_symmetry_vdw_refined0.227
r_nbd_refined0.199
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.11
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms5048
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling