2HMO

Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to 3-Nitrotoluene.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O7H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5279.151.9-2.2 M Ammonium Sulfate, 4-6% Dioxane, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
Crystal Properties
Matthews coefficientSolvent content
2.7154.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.211α = 90
b = 140.211β = 90
c = 208.271γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12004-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.04021ALS4.2.2

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
11.615.9599.20.111.87.07102411102411
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)
1.61.6696.60.432.12.629895

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODY REFINEMENTTHROUGHOUT1O7H1.615.95102382102382512299.070.1620.1620.1610.197RANDOM17.437
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]
0.450.230.45-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.718
r_dihedral_angle_4_deg17.552
r_dihedral_angle_3_deg12.584
r_sphericity_free8.304
r_dihedral_angle_1_deg6.454
r_scangle_it3.095
r_scbond_it2.284
r_sphericity_bonded1.953
r_rigid_bond_restr1.648
r_angle_refined_deg1.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.718
r_dihedral_angle_4_deg17.552
r_dihedral_angle_3_deg12.584
r_sphericity_free8.304
r_dihedral_angle_1_deg6.454
r_scangle_it3.095
r_scbond_it2.284
r_sphericity_bonded1.953
r_rigid_bond_restr1.648
r_angle_refined_deg1.377
r_mcangle_it1.369
r_mcbond_it1.162
r_angle_other_deg0.98
r_mcbond_other0.333
r_symmetry_vdw_other0.243
r_nbd_refined0.209
r_nbd_other0.204
r_symmetry_vdw_refined0.188
r_nbtor_refined0.179
r_metal_ion_refined0.167
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.121
r_chiral_restr0.112
r_nbtor_other0.086
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5089
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms113

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction