2BMR

The Crystal Structure of Nitrobenzene Dioxygenase in complex with 3- nitrotoluene


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M MES PH, 6% PEG 8000 (W/V), 5MM NICL2, 50 MM 3-NITROTOLUENE. THE 3-NITROTOLUENE WAS PREPARED FROM A 1M STOCK SOLUTION WHERE 3-NITROTOLUENE HAS BEEN DISOLVED IN ETHANOL.
Crystal Properties
Matthews coefficientSolvent content
2.0940.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.625α = 90
b = 121.625β = 90
c = 84.002γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-02-14MSINGLE 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
11.560.8698.70.086.73.31084501
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)
11.51.5897.60.333.13.3

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 2BMO1.552.55105435556298.70.170.1690.191RANDOM16.28
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]
-0.28-0.14-0.280.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.252
r_dihedral_angle_4_deg14.723
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg6.235
r_scangle_it2.469
r_scbond_it1.641
r_angle_refined_deg1.301
r_mcangle_it1.052
r_mcbond_it0.64
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.252
r_dihedral_angle_4_deg14.723
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg6.235
r_scangle_it2.469
r_scbond_it1.641
r_angle_refined_deg1.301
r_mcangle_it1.052
r_mcbond_it0.64
r_nbtor_refined0.308
r_symmetry_vdw_refined0.238
r_nbd_refined0.203
r_symmetry_hbond_refined0.123
r_xyhbond_nbd_refined0.104
r_chiral_restr0.09
r_bond_refined_d0.009
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 Atoms5049
Nucleic Acid Atoms
Solvent Atoms727
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling